Name: rs397686431
Published: September 21, 2022
License: Open Access

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.

rs397686431

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:110674005-110674006 (GRCh38.p14) 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: insAG / insT
Variation Type: Insertion
Frequency: insT=0.000014 (2/138604, GnomAD)
insAG=0.00000 (0/11862, ALFA)
insT=0.00000 (0/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TMEM232 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

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: 20230706150541

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

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	138604	- No frequency provided	insT=0.000014
gnomAD - Genomes	European	Sub	74956	- No frequency provided	insT=0.00001
gnomAD - Genomes	African	Sub	41588	- No frequency provided	insT=0.00000
gnomAD - Genomes	American	Sub	13506	- No frequency provided	insT=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	- No frequency provided	insT=0.0000
gnomAD - Genomes	East Asian	Sub	3114	- No frequency provided	insT=0.0000
gnomAD - Genomes	Other	Sub	2122	- No frequency provided	insT=0.0000
Allele Frequency Aggregator	Total	Global	11862	- No frequency provided	insAG=0.00000, insT=0.00000
Allele Frequency Aggregator	European	Sub	7618	- No frequency provided	insAG=0.0000, insT=0.0000
Allele Frequency Aggregator	African	Sub	2816	- No frequency provided	insAG=0.0000, insT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	- No frequency provided	insAG=0.000, insT=0.000
Allele Frequency Aggregator	Other	Sub	470	- No frequency provided	insAG=0.000, insT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	- No frequency provided	insAG=0.000, insT=0.000
Allele Frequency Aggregator	Asian	Sub	108	- No frequency provided	insAG=0.000, insT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	- No frequency provided	insAG=0.00, insT=0.00

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.p14 chr 5	NC_000005.10:g.110674005_110674006insAG
GRCh38.p14 chr 5	NC_000005.10:g.110674005_110674006insT
GRCh37.p13 chr 5	NC_000005.9:g.110009706_110009707insAG
GRCh37.p13 chr 5	NC_000005.9:g.110009706_110009707insT

Gene: TMEM232, transmembrane protein 232 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM232 transcript	NM_001039763.4:c.-12-6642… NM_001039763.4:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X1	XM_006714670.4:c.-12-6642… XM_006714670.4:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X3	XM_011543552.3:c.-12-6642… XM_011543552.3:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X6	XM_011543555.3:c.69-31635… XM_011543555.3:c.69-31635_69-31634insCT	N/A	Intron Variant
TMEM232 transcript variant X7	XM_011543556.3:c.69-31635… XM_011543556.3:c.69-31635_69-31634insCT	N/A	Intron Variant
TMEM232 transcript variant X9	XM_011543557.3:c.-12-6642… XM_011543557.3:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X11	XM_011543559.3:c.-12-6642… XM_011543559.3:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X15	XM_011543561.3:c.-12-6642… XM_011543561.3:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X19	XM_011543563.3:c.-12-6642… XM_011543563.3:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X20	XM_011543565.4:c.-12-6642… XM_011543565.4:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X22	XM_011543567.4:c.-12-6642… XM_011543567.4:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X8	XM_017009705.3:c.-12-6642… XM_017009705.3:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X17	XM_017009706.3:c.-12-6642… XM_017009706.3:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X10	XM_047417491.1:c.-12-6642… XM_047417491.1:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X12	XM_047417492.1:c.-12-6642… XM_047417492.1:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X13	XM_047417493.1:c.-229-316… XM_047417493.1:c.-229-31635_-229-31634insCT	N/A	Intron Variant
TMEM232 transcript variant X16	XM_047417494.1:c.-12-6642… XM_047417494.1:c.-12-6642_-12-6641insCT	N/A	Intron Variant
TMEM232 transcript variant X2	XM_011543553.3:c.	N/A	Genic Upstream Transcript Variant
TMEM232 transcript variant X14	XM_011543560.3:c.	N/A	Genic Upstream Transcript Variant
TMEM232 transcript variant X21	XM_047417495.1:c.	N/A	Genic Upstream Transcript Variant
TMEM232 transcript variant X4	XR_001742181.2:n.	N/A	Intron Variant
TMEM232 transcript variant X18	XR_001742182.2:n.	N/A	Intron Variant
TMEM232 transcript variant X5	XR_007058620.1:n.	N/A	Intron Variant

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

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	=	insAG	insT
GRCh38.p14 chr 5	NC_000005.10:g.110674005_110674006=	NC_000005.10:g.110674005_110674006insAG	NC_000005.10:g.110674005_110674006insT
GRCh37.p13 chr 5	NC_000005.9:g.110009706_110009707=	NC_000005.9:g.110009706_110009707insAG	NC_000005.9:g.110009706_110009707insT
TMEM232 transcript	NM_001039763.3:c.-12-6642=	NM_001039763.3:c.-12-6642_-12-6641insCT	NM_001039763.3:c.-12-6642_-12-6641insA
TMEM232 transcript	NM_001039763.4:c.-12-6642=	NM_001039763.4:c.-12-6642_-12-6641insCT	NM_001039763.4:c.-12-6642_-12-6641insA
TMEM232 transcript variant X1	XM_005272046.1:c.-12-6642=	XM_005272046.1:c.-12-6642_-12-6641insCT	XM_005272046.1:c.-12-6642_-12-6641insA
TMEM232 transcript variant X2	XM_005272047.1:c.-229-31635=	XM_005272047.1:c.-229-31635_-229-31634insCT	XM_005272047.1:c.-229-31635_-229-31634insA
TMEM232 transcript variant X1	XM_006714670.4:c.-12-6642=	XM_006714670.4:c.-12-6642_-12-6641insCT	XM_006714670.4:c.-12-6642_-12-6641insA
TMEM232 transcript variant X3	XM_011543552.3:c.-12-6642=	XM_011543552.3:c.-12-6642_-12-6641insCT	XM_011543552.3:c.-12-6642_-12-6641insA
TMEM232 transcript variant X6	XM_011543555.3:c.69-31635=	XM_011543555.3:c.69-31635_69-31634insCT	XM_011543555.3:c.69-31635_69-31634insA
TMEM232 transcript variant X7	XM_011543556.3:c.69-31635=	XM_011543556.3:c.69-31635_69-31634insCT	XM_011543556.3:c.69-31635_69-31634insA
TMEM232 transcript variant X9	XM_011543557.3:c.-12-6642=	XM_011543557.3:c.-12-6642_-12-6641insCT	XM_011543557.3:c.-12-6642_-12-6641insA
TMEM232 transcript variant X11	XM_011543559.3:c.-12-6642=	XM_011543559.3:c.-12-6642_-12-6641insCT	XM_011543559.3:c.-12-6642_-12-6641insA
TMEM232 transcript variant X15	XM_011543561.3:c.-12-6642=	XM_011543561.3:c.-12-6642_-12-6641insCT	XM_011543561.3:c.-12-6642_-12-6641insA
TMEM232 transcript variant X19	XM_011543563.3:c.-12-6642=	XM_011543563.3:c.-12-6642_-12-6641insCT	XM_011543563.3:c.-12-6642_-12-6641insA
TMEM232 transcript variant X20	XM_011543565.4:c.-12-6642=	XM_011543565.4:c.-12-6642_-12-6641insCT	XM_011543565.4:c.-12-6642_-12-6641insA
TMEM232 transcript variant X22	XM_011543567.4:c.-12-6642=	XM_011543567.4:c.-12-6642_-12-6641insCT	XM_011543567.4:c.-12-6642_-12-6641insA
TMEM232 transcript variant X8	XM_017009705.3:c.-12-6642=	XM_017009705.3:c.-12-6642_-12-6641insCT	XM_017009705.3:c.-12-6642_-12-6641insA
TMEM232 transcript variant X17	XM_017009706.3:c.-12-6642=	XM_017009706.3:c.-12-6642_-12-6641insCT	XM_017009706.3:c.-12-6642_-12-6641insA
TMEM232 transcript variant X10	XM_047417491.1:c.-12-6642=	XM_047417491.1:c.-12-6642_-12-6641insCT	XM_047417491.1:c.-12-6642_-12-6641insA
TMEM232 transcript variant X12	XM_047417492.1:c.-12-6642=	XM_047417492.1:c.-12-6642_-12-6641insCT	XM_047417492.1:c.-12-6642_-12-6641insA
TMEM232 transcript variant X13	XM_047417493.1:c.-229-31635=	XM_047417493.1:c.-229-31635_-229-31634insCT	XM_047417493.1:c.-229-31635_-229-31634insA
TMEM232 transcript variant X16	XM_047417494.1:c.-12-6642=	XM_047417494.1:c.-12-6642_-12-6641insCT	XM_047417494.1:c.-12-6642_-12-6641insA

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#.

1 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4126589192	Apr 26, 2021 (155)
2	gnomAD - Genomes	NC_000005.10 - 110674006	Apr 26, 2021 (155)
3	ALFA	NC_000005.10 - 110674006	Apr 26, 2021 (155)

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
11362032394	NC_000005.10:110674005::AG	NC_000005.10:110674005::AG	(self)
199749590, 11362032394, ss4126589192	NC_000005.10:110674005::T	NC_000005.10:110674005::T	(self)

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

No publications for rs397686431

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs397686431