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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs900711576

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:199295-199325 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
delTCTT(CCTC)4
Variation Type
Indel Insertion and Deletion
Frequency
delTCTT(CCTC)4=0.00025 (5/19738, GnomAD)
delTCTT(CCTC)4=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZMYND11 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 10 NC_000010.11:g.199306_199325del
GRCh37.p13 chr 10 NC_000010.10:g.245246_245265del
ZMYND11 RefSeqGene NG_029960.1:g.69842_69861del
Gene: ZMYND11, zinc finger MYND-type containing 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZMYND11 transcript variant 4 NM_001202464.3:c.117-1058…

NM_001202464.3:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 5 NM_001202465.3:c.117-1058…

NM_001202465.3:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 6 NM_001202466.3:c.117-1058…

NM_001202466.3:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 7 NM_001202467.1:c.117-1058…

NM_001202467.1:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 8 NM_001202468.1:c.117-1058…

NM_001202468.1:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 9 NM_001330057.3:c.65+1301_…

NM_001330057.3:c.65+1301_65+1320del

N/A Intron Variant
ZMYND11 transcript variant 10 NM_001370097.3:c.117-1058…

NM_001370097.3:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 11 NM_001370098.2:c.117-1058…

NM_001370098.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 12 NM_001370099.2:c.117-1058…

NM_001370099.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 13 NM_001370100.5:c.117-1058…

NM_001370100.5:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 14 NM_001370101.2:c.117-1058…

NM_001370101.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 15 NM_001370102.2:c.117-1058…

NM_001370102.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 16 NM_001370103.2:c.117-1058…

NM_001370103.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 17 NM_001370104.2:c.117-1058…

NM_001370104.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 18 NM_001370105.2:c.117-1058…

NM_001370105.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 19 NM_001370106.2:c.117-1058…

NM_001370106.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 20 NM_001370107.2:c.117-1058…

NM_001370107.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 21 NM_001370108.2:c.117-1058…

NM_001370108.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 22 NM_001370109.2:c.117-1058…

NM_001370109.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 23 NM_001370110.2:c.117-1058…

NM_001370110.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 24 NM_001370111.2:c.117-1058…

NM_001370111.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 25 NM_001370112.2:c.65+1301_…

NM_001370112.2:c.65+1301_65+1320del

N/A Intron Variant
ZMYND11 transcript variant 26 NM_001370113.2:c.117-1058…

NM_001370113.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 27 NM_001370114.2:c.117-1058…

NM_001370114.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 28 NM_001370115.2:c.117-1058…

NM_001370115.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 29 NM_001370116.2:c.51-10583…

NM_001370116.2:c.51-10583_51-10564del

N/A Intron Variant
ZMYND11 transcript variant 30 NM_001370117.2:c.117-1058…

NM_001370117.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 31 NM_001370118.2:c.-4-10583…

NM_001370118.2:c.-4-10583_-4-10564del

N/A Intron Variant
ZMYND11 transcript variant 32 NM_001370119.2:c.117-1058…

NM_001370119.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 33 NM_001370120.2:c.51-10583…

NM_001370120.2:c.51-10583_51-10564del

N/A Intron Variant
ZMYND11 transcript variant 34 NM_001370121.2:c.-4-10583…

NM_001370121.2:c.-4-10583_-4-10564del

N/A Intron Variant
ZMYND11 transcript variant 35 NM_001370122.2:c.117-1058…

NM_001370122.2:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 36 NM_001370123.2:c.65+1301_…

NM_001370123.2:c.65+1301_65+1320del

N/A Intron Variant
ZMYND11 transcript variant 37 NM_001370124.3:c.-33-3753…

NM_001370124.3:c.-33-37532_-33-37513del

N/A Intron Variant
ZMYND11 transcript variant 1 NM_006624.7:c.117-10583_1…

NM_006624.7:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 2 NM_212479.4:c.117-10583_1…

NM_212479.4:c.117-10583_117-10564del

N/A Intron Variant
ZMYND11 transcript variant 38 NR_163254.2:n. N/A Intron Variant
ZMYND11 transcript variant X12 XM_017015594.1:c.65+1301_…

XM_017015594.1:c.65+1301_65+1320del

N/A Intron Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.00000 CTCCCTCCCTC=0.00000
European Sub 7618 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.0000 CTCCCTCCCTC=0.0000
African Sub 2816 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.0000 CTCCCTCCCTC=0.0000
African Others Sub 108 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.000 CTCCCTCCCTC=0.000
African American Sub 2708 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.0000 CTCCCTCCCTC=0.0000
Asian Sub 108 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.000 CTCCCTCCCTC=0.000
East Asian Sub 84 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.00 CTCCCTCCCTC=0.00
Other Asian Sub 24 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.00 CTCCCTCCCTC=0.00
Latin American 1 Sub 146 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.000 CTCCCTCCCTC=0.000
Latin American 2 Sub 610 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.000 CTCCCTCCCTC=0.000
South Asian Sub 94 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.00 CTCCCTCCCTC=0.00
Other Sub 470 CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC=1.000 CTCCCTCCCTC=0.000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 19738 (CTCC)2(CT)3(TCC)2CTCCCTCCCTC=0.99975 delTCTT(CCTC)4=0.00025
gnomAD - Genomes European Sub 11210 (CTCC)2(CT)3(TCC)2CTCCCTCCCTC=0.99964 delTCTT(CCTC)4=0.00036
gnomAD - Genomes African Sub 5894 (CTCC)2(CT)3(TCC)2CTCCCTCCCTC=0.9998 delTCTT(CCTC)4=0.0002
gnomAD - Genomes American Sub 1364 (CTCC)2(CT)3(TCC)2CTCCCTCCCTC=1.0000 delTCTT(CCTC)4=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 552 (CTCC)2(CT)3(TCC)2CTCCCTCCCTC=1.000 delTCTT(CCTC)4=0.000
gnomAD - Genomes East Asian Sub 398 (CTCC)2(CT)3(TCC)2CTCCCTCCCTC=1.000 delTCTT(CCTC)4=0.000
gnomAD - Genomes Other Sub 320 (CTCC)2(CT)3(TCC)2CTCCCTCCCTC=1.000 delTCTT(CCTC)4=0.000
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement (CTCC)2(CT)3(TCC)2CTCCCTCCCTC= delTCTT(CCTC)4
GRCh38.p13 chr 10 NC_000010.11:g.199295_199325= NC_000010.11:g.199306_199325del
GRCh37.p13 chr 10 NC_000010.10:g.245235_245265= NC_000010.10:g.245246_245265del
ZMYND11 RefSeqGene NG_029960.1:g.69831_69861= NG_029960.1:g.69842_69861del
ZMYND11 transcript variant 4 NM_001202464.1:c.117-10594= NM_001202464.1:c.117-10583_117-10564del
ZMYND11 transcript variant 4 NM_001202464.3:c.117-10594= NM_001202464.3:c.117-10583_117-10564del
ZMYND11 transcript variant 5 NM_001202465.1:c.117-10594= NM_001202465.1:c.117-10583_117-10564del
ZMYND11 transcript variant 5 NM_001202465.3:c.117-10594= NM_001202465.3:c.117-10583_117-10564del
ZMYND11 transcript variant 6 NM_001202466.1:c.117-10594= NM_001202466.1:c.117-10583_117-10564del
ZMYND11 transcript variant 6 NM_001202466.3:c.117-10594= NM_001202466.3:c.117-10583_117-10564del
ZMYND11 transcript variant 7 NM_001202467.1:c.117-10594= NM_001202467.1:c.117-10583_117-10564del
ZMYND11 transcript variant 8 NM_001202468.1:c.117-10594= NM_001202468.1:c.117-10583_117-10564del
ZMYND11 transcript variant 9 NM_001330057.3:c.65+1290= NM_001330057.3:c.65+1301_65+1320del
ZMYND11 transcript variant 10 NM_001370097.3:c.117-10594= NM_001370097.3:c.117-10583_117-10564del
ZMYND11 transcript variant 11 NM_001370098.2:c.117-10594= NM_001370098.2:c.117-10583_117-10564del
ZMYND11 transcript variant 12 NM_001370099.2:c.117-10594= NM_001370099.2:c.117-10583_117-10564del
ZMYND11 transcript variant 13 NM_001370100.5:c.117-10594= NM_001370100.5:c.117-10583_117-10564del
ZMYND11 transcript variant 14 NM_001370101.2:c.117-10594= NM_001370101.2:c.117-10583_117-10564del
ZMYND11 transcript variant 15 NM_001370102.2:c.117-10594= NM_001370102.2:c.117-10583_117-10564del
ZMYND11 transcript variant 16 NM_001370103.2:c.117-10594= NM_001370103.2:c.117-10583_117-10564del
ZMYND11 transcript variant 17 NM_001370104.2:c.117-10594= NM_001370104.2:c.117-10583_117-10564del
ZMYND11 transcript variant 18 NM_001370105.2:c.117-10594= NM_001370105.2:c.117-10583_117-10564del
ZMYND11 transcript variant 19 NM_001370106.2:c.117-10594= NM_001370106.2:c.117-10583_117-10564del
ZMYND11 transcript variant 20 NM_001370107.2:c.117-10594= NM_001370107.2:c.117-10583_117-10564del
ZMYND11 transcript variant 21 NM_001370108.2:c.117-10594= NM_001370108.2:c.117-10583_117-10564del
ZMYND11 transcript variant 22 NM_001370109.2:c.117-10594= NM_001370109.2:c.117-10583_117-10564del
ZMYND11 transcript variant 23 NM_001370110.2:c.117-10594= NM_001370110.2:c.117-10583_117-10564del
ZMYND11 transcript variant 24 NM_001370111.2:c.117-10594= NM_001370111.2:c.117-10583_117-10564del
ZMYND11 transcript variant 25 NM_001370112.2:c.65+1290= NM_001370112.2:c.65+1301_65+1320del
ZMYND11 transcript variant 26 NM_001370113.2:c.117-10594= NM_001370113.2:c.117-10583_117-10564del
ZMYND11 transcript variant 27 NM_001370114.2:c.117-10594= NM_001370114.2:c.117-10583_117-10564del
ZMYND11 transcript variant 28 NM_001370115.2:c.117-10594= NM_001370115.2:c.117-10583_117-10564del
ZMYND11 transcript variant 29 NM_001370116.2:c.51-10594= NM_001370116.2:c.51-10583_51-10564del
ZMYND11 transcript variant 30 NM_001370117.2:c.117-10594= NM_001370117.2:c.117-10583_117-10564del
ZMYND11 transcript variant 31 NM_001370118.2:c.-4-10594= NM_001370118.2:c.-4-10583_-4-10564del
ZMYND11 transcript variant 32 NM_001370119.2:c.117-10594= NM_001370119.2:c.117-10583_117-10564del
ZMYND11 transcript variant 33 NM_001370120.2:c.51-10594= NM_001370120.2:c.51-10583_51-10564del
ZMYND11 transcript variant 34 NM_001370121.2:c.-4-10594= NM_001370121.2:c.-4-10583_-4-10564del
ZMYND11 transcript variant 35 NM_001370122.2:c.117-10594= NM_001370122.2:c.117-10583_117-10564del
ZMYND11 transcript variant 36 NM_001370123.2:c.65+1290= NM_001370123.2:c.65+1301_65+1320del
ZMYND11 transcript variant 37 NM_001370124.3:c.-33-37543= NM_001370124.3:c.-33-37532_-33-37513del
ZMYND11 transcript variant 1 NM_006624.5:c.117-10594= NM_006624.5:c.117-10583_117-10564del
ZMYND11 transcript variant 1 NM_006624.7:c.117-10594= NM_006624.7:c.117-10583_117-10564del
ZMYND11 transcript variant 2 NM_212479.3:c.117-10594= NM_212479.3:c.117-10583_117-10564del
ZMYND11 transcript variant 2 NM_212479.4:c.117-10594= NM_212479.4:c.117-10583_117-10564del
ZMYND11 transcript variant X1 XM_005252359.1:c.117-10594= XM_005252359.1:c.117-10583_117-10564del
ZMYND11 transcript variant X2 XM_005252360.1:c.117-10594= XM_005252360.1:c.117-10583_117-10564del
ZMYND11 transcript variant X3 XM_005252361.1:c.117-10594= XM_005252361.1:c.117-10583_117-10564del
ZMYND11 transcript variant X5 XM_005252362.1:c.117-10594= XM_005252362.1:c.117-10583_117-10564del
ZMYND11 transcript variant X5 XM_005252363.1:c.117-10594= XM_005252363.1:c.117-10583_117-10564del
ZMYND11 transcript variant X12 XM_017015594.1:c.65+1290= XM_017015594.1:c.65+1301_65+1320del
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

3 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss2136342934 Dec 20, 2016 (150)
2 TOPMED ss3109354073 Nov 08, 2017 (151)
3 GNOMAD ss4211433089 Apr 26, 2021 (155)
4 gnomAD - Genomes NC_000010.11 - 199295 Apr 26, 2021 (155)
5 ALFA NC_000010.11 - 199295 Apr 26, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2136342934 NC_000010.10:245234:CTCCCTCCCTCTCT…

NC_000010.10:245234:CTCCCTCCCTCTCTTCCTCC:

NC_000010.11:199294:CTCCCTCCCTCTCT…

NC_000010.11:199294:CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC:CTCCCTCCCTC

(self)
340958038, ss3109354073, ss4211433089 NC_000010.11:199294:CTCCCTCCCTCTCT…

NC_000010.11:199294:CTCCCTCCCTCTCTTCCTCC:

NC_000010.11:199294:CTCCCTCCCTCTCT…

NC_000010.11:199294:CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC:CTCCCTCCCTC

(self)
8058217172 NC_000010.11:199294:CTCCCTCCCTCTCT…

NC_000010.11:199294:CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC:CTCCCTCCCTC

NC_000010.11:199294:CTCCCTCCCTCTCT…

NC_000010.11:199294:CTCCCTCCCTCTCTTCCTCCCTCCCTCCCTC:CTCCCTCCCTC

Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs900711576

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad