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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.

rs16987048

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr19:56190081 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.004582 (1145/249916, GnomAD_exome)
G=0.001472 (318/216042, ALFA)
G=0.019446 (2726/140182, GnomAD) (+ 10 more)
G=0.005687 (687/120796, ExAC)
G=0.02920 (2298/78698, PAGE_STUDY)
G=0.01923 (248/12898, GO-ESP)
G=0.0202 (101/5008, 1000G)
G=0.0002 (1/4480, Estonian)
G=0.0005 (2/3854, ALSPAC)
G=0.0003 (1/3708, TWINSUK)
G=0.067 (67/1000, HapMap)
G=0.019 (4/216, Qatari)
T=0.44 (8/18, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZSCAN5B : Missense 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 19 NC_000019.10:g.56190081T>C
GRCh38.p13 chr 19 NC_000019.10:g.56190081T>G
GRCh37.p13 chr 19 NC_000019.9:g.56701450T>C
GRCh37.p13 chr 19 NC_000019.9:g.56701450T>G
Gene: ZSCAN5B, zinc finger and SCAN domain containing 5B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZSCAN5B transcript variant 1 NM_001080456.3:c.1234A>G M [ATG] > V [GTG] Coding Sequence Variant
zinc finger and SCAN domain-containing protein 5B NP_001073925.2:p.Met412Val M (Met) > V (Val) Missense Variant
ZSCAN5B transcript variant 1 NM_001080456.3:c.1234A>C M [ATG] > L [CTG] Coding Sequence Variant
zinc finger and SCAN domain-containing protein 5B NP_001073925.2:p.Met412Leu M (Met) > L (Leu) Missense Variant
ZSCAN5B transcript variant 2 NM_001385638.1:c.1234A>G M [ATG] > V [GTG] Coding Sequence Variant
zinc finger and SCAN domain-containing protein 5B NP_001372567.1:p.Met412Val M (Met) > V (Val) Missense Variant
ZSCAN5B transcript variant 2 NM_001385638.1:c.1234A>C M [ATG] > L [CTG] Coding Sequence Variant
zinc finger and SCAN domain-containing protein 5B NP_001372567.1:p.Met412Leu M (Met) > L (Leu) Missense 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 (New)
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 216042 T=0.998528 C=0.000000, G=0.001472
European Sub 184918 T=0.999746 C=0.000000, G=0.000254
African Sub 6068 T=0.9654 C=0.0000, G=0.0346
African Others Sub 208 T=0.933 C=0.000, G=0.067
African American Sub 5860 T=0.9666 C=0.0000, G=0.0334
Asian Sub 6366 T=1.0000 C=0.0000, G=0.0000
East Asian Sub 4516 T=1.0000 C=0.0000, G=0.0000
Other Asian Sub 1850 T=1.0000 C=0.0000, G=0.0000
Latin American 1 Sub 812 T=0.982 C=0.000, G=0.018
Latin American 2 Sub 1056 T=0.9972 C=0.0000, G=0.0028
South Asian Sub 296 T=1.000 C=0.000, G=0.000
Other Sub 16526 T=0.99740 C=0.00000, G=0.00260


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 - Exomes Global Study-wide 249916 T=0.995418 G=0.004582
gnomAD - Exomes European Sub 134844 T=0.999740 G=0.000260
gnomAD - Exomes Asian Sub 48856 T=0.99996 G=0.00004
gnomAD - Exomes American Sub 34566 T=0.99685 G=0.00315
gnomAD - Exomes African Sub 15516 T=0.93639 G=0.06361
gnomAD - Exomes Ashkenazi Jewish Sub 10068 T=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6066 T=0.9980 G=0.0020
gnomAD - Genomes Global Study-wide 140182 T=0.980554 G=0.019446
gnomAD - Genomes European Sub 75942 T=0.99980 G=0.00020
gnomAD - Genomes African Sub 42004 T=0.93832 G=0.06168
gnomAD - Genomes American Sub 13638 T=0.99369 G=0.00631
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3128 T=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 T=0.9842 G=0.0158
ExAC Global Study-wide 120796 T=0.994313 G=0.005687
ExAC Europe Sub 73352 T=0.99969 G=0.00031
ExAC Asian Sub 25148 T=0.99996 G=0.00004
ExAC American Sub 11574 T=0.99654 G=0.00346
ExAC African Sub 9820 T=0.9367 G=0.0633
ExAC Other Sub 902 T=0.999 G=0.001
The PAGE Study Global Study-wide 78698 T=0.97080 G=0.02920
The PAGE Study AfricanAmerican Sub 32514 T=0.94138 G=0.05862
The PAGE Study Mexican Sub 10810 T=0.99685 G=0.00315
The PAGE Study Asian Sub 8318 T=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7918 T=0.9830 G=0.0170
The PAGE Study NativeHawaiian Sub 4532 T=0.9996 G=0.0004
The PAGE Study Cuban Sub 4230 T=0.9875 G=0.0125
The PAGE Study Dominican Sub 3828 T=0.9684 G=0.0316
The PAGE Study CentralAmerican Sub 2450 T=0.9878 G=0.0122
The PAGE Study SouthAmerican Sub 1982 T=0.9939 G=0.0061
The PAGE Study NativeAmerican Sub 1260 T=0.9960 G=0.0040
The PAGE Study SouthAsian Sub 856 T=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 12898 T=0.98077 G=0.01923
GO Exome Sequencing Project European American Sub 8552 T=0.9998 G=0.0002
GO Exome Sequencing Project African American Sub 4346 T=0.9434 G=0.0566
1000Genomes Global Study-wide 5008 T=0.9798 G=0.0202
1000Genomes African Sub 1322 T=0.9274 G=0.0726
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=1.0000 G=0.0000
1000Genomes South Asian Sub 978 T=1.000 G=0.000
1000Genomes American Sub 694 T=0.993 G=0.007
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9998 G=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9995 G=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9997 G=0.0003
HapMap Global Study-wide 1000 T=0.933 G=0.067
HapMap African Sub 692 T=0.916 G=0.084
HapMap American Sub 218 T=0.959 G=0.041
HapMap Asian Sub 90 T=1.00 G=0.00
Qatari Global Study-wide 216 T=0.981 G=0.019
SGDP_PRJ Global Study-wide 18 T=0.44 G=0.56
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 T= C G
GRCh38.p13 chr 19 NC_000019.10:g.56190081= NC_000019.10:g.56190081T>C NC_000019.10:g.56190081T>G
GRCh37.p13 chr 19 NC_000019.9:g.56701450= NC_000019.9:g.56701450T>C NC_000019.9:g.56701450T>G
ZSCAN5B transcript variant 1 NM_001080456.3:c.1234= NM_001080456.3:c.1234A>G NM_001080456.3:c.1234A>C
ZSCAN5B transcript NM_001080456.2:c.1234= NM_001080456.2:c.1234A>G NM_001080456.2:c.1234A>C
ZSCAN5B transcript variant 2 NM_001385638.1:c.1234= NM_001385638.1:c.1234A>G NM_001385638.1:c.1234A>C
zinc finger and SCAN domain-containing protein 5B NP_001073925.2:p.Met412= NP_001073925.2:p.Met412Val NP_001073925.2:p.Met412Leu
zinc finger and SCAN domain-containing protein 5B NP_001372567.1:p.Met412= NP_001372567.1:p.Met412Val NP_001372567.1:p.Met412Leu
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#.

64 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23771740 Sep 20, 2004 (123)
2 PERLEGEN ss69231983 May 16, 2007 (127)
3 ILLUMINA ss74855122 Dec 07, 2007 (129)
4 KRIBB_YJKIM ss119861370 Dec 01, 2009 (131)
5 ILLUMINA ss172693555 Jul 04, 2010 (132)
6 1000GENOMES ss228201242 Jul 14, 2010 (132)
7 ILLUMINA ss482336285 May 04, 2012 (137)
8 ILLUMINA ss483854973 May 04, 2012 (137)
9 1000GENOMES ss491169092 May 04, 2012 (137)
10 EXOME_CHIP ss491555392 May 04, 2012 (137)
11 ILLUMINA ss534603297 Sep 08, 2015 (146)
12 NHLBI-ESP ss713543021 Apr 25, 2013 (138)
13 ILLUMINA ss779121083 Aug 21, 2014 (142)
14 ILLUMINA ss780750742 Aug 21, 2014 (142)
15 ILLUMINA ss781727927 Aug 21, 2014 (142)
16 ILLUMINA ss783428816 Aug 21, 2014 (142)
17 ILLUMINA ss834585426 Aug 21, 2014 (142)
18 JMKIDD_LAB ss974508236 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1067594738 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1081996330 Aug 21, 2014 (142)
21 1000GENOMES ss1363692982 Aug 21, 2014 (142)
22 EVA_UK10K_ALSPAC ss1638212423 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1681206456 Apr 01, 2015 (144)
24 EVA_EXAC ss1693834682 Apr 01, 2015 (144)
25 EVA_DECODE ss1698490713 Apr 01, 2015 (144)
26 ILLUMINA ss1752296171 Sep 08, 2015 (146)
27 ILLUMINA ss1917942752 Feb 12, 2016 (147)
28 WEILL_CORNELL_DGM ss1937945583 Feb 12, 2016 (147)
29 ILLUMINA ss1946543132 Feb 12, 2016 (147)
30 ILLUMINA ss1959886810 Feb 12, 2016 (147)
31 HUMAN_LONGEVITY ss2226693485 Dec 20, 2016 (150)
32 TOPMED ss2392584544 Dec 20, 2016 (150)
33 ILLUMINA ss2633557201 Nov 08, 2017 (151)
34 GNOMAD ss2744357374 Nov 08, 2017 (151)
35 GNOMAD ss2750305169 Nov 08, 2017 (151)
36 GNOMAD ss2964389035 Nov 08, 2017 (151)
37 AFFY ss2985154872 Nov 08, 2017 (151)
38 ILLUMINA ss3021928279 Nov 08, 2017 (151)
39 TOPMED ss3296726072 Nov 08, 2017 (151)
40 ILLUMINA ss3627966501 Oct 12, 2018 (152)
41 ILLUMINA ss3627966502 Oct 12, 2018 (152)
42 ILLUMINA ss3631527068 Oct 12, 2018 (152)
43 ILLUMINA ss3634745614 Oct 12, 2018 (152)
44 ILLUMINA ss3638236367 Oct 12, 2018 (152)
45 ILLUMINA ss3640452919 Oct 12, 2018 (152)
46 ILLUMINA ss3643208322 Oct 12, 2018 (152)
47 ILLUMINA ss3644731641 Oct 12, 2018 (152)
48 ILLUMINA ss3652356201 Oct 12, 2018 (152)
49 ILLUMINA ss3653925343 Oct 12, 2018 (152)
50 EGCUT_WGS ss3684427861 Jul 13, 2019 (153)
51 ILLUMINA ss3725746482 Jul 13, 2019 (153)
52 ILLUMINA ss3744470076 Jul 13, 2019 (153)
53 ILLUMINA ss3745045601 Jul 13, 2019 (153)
54 PAGE_CC ss3772027619 Jul 13, 2019 (153)
55 ILLUMINA ss3772542565 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3821476681 Jul 13, 2019 (153)
57 EVA ss3825336331 Apr 27, 2020 (154)
58 EVA ss3825945347 Apr 27, 2020 (154)
59 SGDP_PRJ ss3888528397 Apr 27, 2020 (154)
60 FSA-LAB ss3984165519 Apr 26, 2021 (155)
61 EVA ss3986817648 Apr 26, 2021 (155)
62 EVA ss4017831945 Apr 26, 2021 (155)
63 TOPMED ss5079104720 Apr 26, 2021 (155)
64 TOPMED ss5079104721 Apr 26, 2021 (155)
65 1000Genomes NC_000019.9 - 56701450 Oct 12, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 56701450 Oct 12, 2018 (152)
67 Genetic variation in the Estonian population NC_000019.9 - 56701450 Oct 12, 2018 (152)
68 ExAC NC_000019.9 - 56701450 Oct 12, 2018 (152)
69 gnomAD - Genomes NC_000019.10 - 56190081 Apr 26, 2021 (155)
70 gnomAD - Exomes NC_000019.9 - 56701450 Jul 13, 2019 (153)
71 GO Exome Sequencing Project NC_000019.9 - 56701450 Oct 12, 2018 (152)
72 HapMap NC_000019.10 - 56190081 Apr 27, 2020 (154)
73 The PAGE Study NC_000019.10 - 56190081 Jul 13, 2019 (153)
74 Qatari NC_000019.9 - 56701450 Apr 27, 2020 (154)
75 SGDP_PRJ NC_000019.9 - 56701450 Apr 27, 2020 (154)
76 TopMed

Submission ignored due to conflicting rows:
Row 294650384 (NC_000019.10:56190080:T:C 1/264690)
Row 294650385 (NC_000019.10:56190080:T:G 5257/264690)

- Apr 26, 2021 (155)
77 TopMed

Submission ignored due to conflicting rows:
Row 294650384 (NC_000019.10:56190080:T:C 1/264690)
Row 294650385 (NC_000019.10:56190080:T:G 5257/264690)

- Apr 26, 2021 (155)
78 UK 10K study - Twins NC_000019.9 - 56701450 Oct 12, 2018 (152)
79 ALFA NC_000019.10 - 56190081 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
15186221674, ss5079104720 NC_000019.10:56190080:T:C NC_000019.10:56190080:T:C
ss483854973, ss1698490713, ss3643208322 NC_000019.8:61393261:T:G NC_000019.10:56190080:T:G (self)
77119729, 42684443, 30166109, 4356358, 13673273, 1793264, 19987505, 40545377, 42684443, ss228201242, ss482336285, ss491169092, ss491555392, ss534603297, ss713543021, ss779121083, ss780750742, ss781727927, ss783428816, ss834585426, ss974508236, ss1067594738, ss1081996330, ss1363692982, ss1638212423, ss1681206456, ss1693834682, ss1752296171, ss1917942752, ss1937945583, ss1946543132, ss1959886810, ss2392584544, ss2633557201, ss2744357374, ss2750305169, ss2964389035, ss2985154872, ss3021928279, ss3627966501, ss3627966502, ss3631527068, ss3634745614, ss3638236367, ss3640452919, ss3644731641, ss3652356201, ss3653925343, ss3684427861, ss3744470076, ss3745045601, ss3772542565, ss3825336331, ss3825945347, ss3888528397, ss3984165519, ss3986817648, ss4017831945 NC_000019.9:56701449:T:G NC_000019.10:56190080:T:G (self)
543835690, 1715512, 1249088, 183791031, 15186221674, ss2226693485, ss3296726072, ss3725746482, ss3772027619, ss3821476681, ss5079104721 NC_000019.10:56190080:T:G NC_000019.10:56190080:T:G (self)
ss23771740, ss69231983, ss74855122, ss119861370, ss172693555 NT_011109.16:28969667:T:G NC_000019.10:56190080:T:G (self)
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 rs16987048

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