Name: rs142098064
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.

rs142098064

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:23640804 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.00150 (28/18712, ALFA)
T=0.0030 (19/6404, 1000G_30x)
T=0.0028 (14/5008, 1000G) (+ 8 more)
T=0.0069 (31/4480, Estonian)
T=0.0062 (24/3854, ALSPAC)
T=0.0057 (21/3708, TWINSUK)
T=0.005 (5/998, GoNL)
T=0.005 (3/600, NorthernSweden)
T=0.005 (1/216, Qatari)
G=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PALB2 : Intron Variant
DCTN5 : 2KB Upstream 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	18712	G=0.99850	A=0.00000, C=0.00000, T=0.00150
European	Sub	14130	G=0.99802	A=0.00000, C=0.00000, T=0.00198
African	Sub	2938	G=1.0000	A=0.0000, C=0.0000, T=0.0000
African Others	Sub	114	G=1.000	A=0.000, C=0.000, T=0.000
African American	Sub	2824	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Asian	Sub	112	G=1.000	A=0.000, C=0.000, T=0.000
East Asian	Sub	86	G=1.00	A=0.00, C=0.00, T=0.00
Other Asian	Sub	26	G=1.00	A=0.00, C=0.00, T=0.00
Latin American 1	Sub	144	G=1.000	A=0.000, C=0.000, T=0.000
Latin American 2	Sub	608	G=1.000	A=0.000, C=0.000, T=0.000
South Asian	Sub	96	G=1.00	A=0.00, C=0.00, T=0.00
Other	Sub	684	G=1.000	A=0.000, C=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
Allele Frequency Aggregator	Total	Global	18712	G=0.99850	A=0.00000, C=0.00000, T=0.00150
Allele Frequency Aggregator	European	Sub	14130	G=0.99802	A=0.00000, C=0.00000, T=0.00198
Allele Frequency Aggregator	African	Sub	2938	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	684	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	608	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	144	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	96	G=1.00	A=0.00, C=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9970	T=0.0030
1000Genomes_30x	African	Sub	1786	G=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	G=0.9961	T=0.0039
1000Genomes_30x	South Asian	Sub	1202	G=0.9975	T=0.0025
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	G=0.989	T=0.011
1000Genomes	Global	Study-wide	5008	G=0.9972	T=0.0028
1000Genomes	African	Sub	1322	G=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	G=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	G=0.9960	T=0.0040
1000Genomes	South Asian	Sub	978	G=0.997	T=0.003
1000Genomes	American	Sub	694	G=0.990	T=0.010
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9931	T=0.0069
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9938	T=0.0062
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9943	T=0.0057
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.995	T=0.005
Northern Sweden	ACPOP	Study-wide	600	G=0.995	T=0.005
Qatari	Global	Study-wide	216	G=0.995	T=0.005
SGDP_PRJ	Global	Study-wide	2	G=0.5	T=0.5

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 16	NC_000016.10:g.23640804G>A
GRCh38.p14 chr 16	NC_000016.10:g.23640804G>C
GRCh38.p14 chr 16	NC_000016.10:g.23640804G>T
GRCh37.p13 chr 16	NC_000016.9:g.23652125G>A
GRCh37.p13 chr 16	NC_000016.9:g.23652125G>C
GRCh37.p13 chr 16	NC_000016.9:g.23652125G>T
PALB2 RefSeqGene (LRG_308)	NG_007406.1:g.5554C>T
PALB2 RefSeqGene (LRG_308)	NG_007406.1:g.5554C>G
PALB2 RefSeqGene (LRG_308)	NG_007406.1:g.5554C>A

Gene: PALB2, partner and localizer of BRCA2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PALB2 transcript variant 1	NM_024675.4:c.48+306C>T	N/A	Intron Variant
PALB2 transcript variant X4	XM_011545948.3:c.-972+306… XM_011545948.3:c.-972+306C>T	N/A	Intron Variant
PALB2 transcript variant X3	XM_017023673.3:c.48+306C>T	N/A	Intron Variant
PALB2 transcript variant X1	XM_011545946.3:c.-499=	N/A	5 Prime UTR Variant
PALB2 transcript variant X2	XM_011545947.3:c.-499=	N/A	5 Prime UTR Variant

Gene: DCTN5, dynactin subunit 5 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
DCTN5 transcript variant 2	NM_001199011.2:c.	N/A	Upstream Transcript Variant
DCTN5 transcript variant 4	NM_001199743.2:c.	N/A	Upstream Transcript Variant
DCTN5 transcript variant 1	NM_032486.4:c.	N/A	Upstream Transcript Variant
DCTN5 transcript variant 3	NR_037573.2:n.	N/A	Upstream Transcript Variant
DCTN5 transcript variant X1	XR_001752006.3:n.	N/A	Upstream Transcript Variant
DCTN5 transcript variant X2	XR_001752007.3:n.	N/A	Upstream Transcript 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	G=	A	C	T
GRCh38.p14 chr 16	NC_000016.10:g.23640804=	NC_000016.10:g.23640804G>A	NC_000016.10:g.23640804G>C	NC_000016.10:g.23640804G>T
GRCh37.p13 chr 16	NC_000016.9:g.23652125=	NC_000016.9:g.23652125G>A	NC_000016.9:g.23652125G>C	NC_000016.9:g.23652125G>T
PALB2 RefSeqGene (LRG_308)	NG_007406.1:g.5554=	NG_007406.1:g.5554C>T	NG_007406.1:g.5554C>G	NG_007406.1:g.5554C>A
PALB2 transcript variant 9	NM_001407304.1:c.-1390=	NM_001407304.1:c.-1390C>T	NM_001407304.1:c.-1390C>G	NM_001407304.1:c.-1390C>A
PALB2 transcript variant 15	NM_001407310.1:c.-1390=	NM_001407310.1:c.-1390C>T	NM_001407310.1:c.-1390C>G	NM_001407310.1:c.-1390C>A
PALB2 transcript variant X1	XM_011545946.3:c.-499=	XM_011545946.3:c.-499C>T	XM_011545946.3:c.-499C>G	XM_011545946.3:c.-499C>A
PALB2 transcript variant X1	XM_011545946.2:c.-499=	XM_011545946.2:c.-499C>T	XM_011545946.2:c.-499C>G	XM_011545946.2:c.-499C>A
PALB2 transcript variant X1	XM_011545946.1:c.-499=	XM_011545946.1:c.-499C>T	XM_011545946.1:c.-499C>G	XM_011545946.1:c.-499C>A
PALB2 transcript variant X2	XM_011545947.3:c.-499=	XM_011545947.3:c.-499C>T	XM_011545947.3:c.-499C>G	XM_011545947.3:c.-499C>A
PALB2 transcript variant X4	XM_011545947.2:c.-499=	XM_011545947.2:c.-499C>T	XM_011545947.2:c.-499C>G	XM_011545947.2:c.-499C>A
PALB2 transcript variant X2	XM_011545947.1:c.-499=	XM_011545947.1:c.-499C>T	XM_011545947.1:c.-499C>G	XM_011545947.1:c.-499C>A
PALB2 transcript	NM_024675.3:c.48+306=	NM_024675.3:c.48+306C>T	NM_024675.3:c.48+306C>G	NM_024675.3:c.48+306C>A
PALB2 transcript variant 1	NM_024675.4:c.48+306=	NM_024675.4:c.48+306C>T	NM_024675.4:c.48+306C>G	NM_024675.4:c.48+306C>A
PALB2 transcript variant X1	XM_005255578.1:c.48+306=	XM_005255578.1:c.48+306C>T	XM_005255578.1:c.48+306C>G	XM_005255578.1:c.48+306C>A
PALB2 transcript variant X4	XM_011545948.3:c.-972+306=	XM_011545948.3:c.-972+306C>T	XM_011545948.3:c.-972+306C>G	XM_011545948.3:c.-972+306C>A
PALB2 transcript variant X3	XM_017023673.3:c.48+306=	XM_017023673.3:c.48+306C>T	XM_017023673.3:c.48+306C>G	XM_017023673.3:c.48+306C>A

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#.

24 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss339180196	May 09, 2011 (134)
2	EVA-GONL	ss992382825	Aug 21, 2014 (142)
3	1000GENOMES	ss1355779408	Aug 21, 2014 (142)
4	EVA_UK10K_ALSPAC	ss1634205674	Apr 01, 2015 (144)
5	EVA_UK10K_TWINSUK	ss1677199707	Apr 01, 2015 (144)
6	WEILL_CORNELL_DGM	ss1935805701	Feb 12, 2016 (147)
7	HUMAN_LONGEVITY	ss2211355777	Dec 20, 2016 (150)
8	GNOMAD	ss2941513356	Nov 08, 2017 (151)
9	SWEGEN	ss3014246709	Nov 08, 2017 (151)
10	EGCUT_WGS	ss3681333970	Jul 13, 2019 (153)
11	EVA_DECODE	ss3699034871	Jul 13, 2019 (153)
12	ACPOP	ss3741422564	Jul 13, 2019 (153)
13	SGDP_PRJ	ss3884173225	Apr 27, 2020 (154)
14	TOPMED	ss5011121962	Apr 26, 2021 (155)
15	TOPMED	ss5011121963	Apr 26, 2021 (155)
16	TOPMED	ss5011121964	Apr 26, 2021 (155)
17	1000G_HIGH_COVERAGE	ss5300504262	Oct 16, 2022 (156)
18	EVA	ss5422951686	Oct 16, 2022 (156)
19	HUGCELL_USP	ss5493957086	Oct 16, 2022 (156)
20	1000G_HIGH_COVERAGE	ss5602909054	Oct 16, 2022 (156)
21	SANFORD_IMAGENETICS	ss5658668760	Oct 16, 2022 (156)
22	EVA	ss5846244225	Oct 16, 2022 (156)
23	EVA	ss5898656194	Oct 16, 2022 (156)
24	EVA	ss5950086425	Oct 16, 2022 (156)
25	1000Genomes	NC_000016.9 - 23652125	Oct 12, 2018 (152)
26	1000Genomes_30x	NC_000016.10 - 23640804	Oct 16, 2022 (156)
27	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 23652125	Oct 12, 2018 (152)
28	Genetic variation in the Estonian population	NC_000016.9 - 23652125	Oct 12, 2018 (152)
29	gnomAD - Genomes Submission ignored due to conflicting rows: Row 485803415 (NC_000016.10:23640803:G:A 1/140220) Row 485803416 (NC_000016.10:23640803:G:C 2/140220) Row 485803417 (NC_000016.10:23640803:G:T 759/140220)	-	Apr 26, 2021 (155)
30	gnomAD - Genomes Submission ignored due to conflicting rows: Row 485803415 (NC_000016.10:23640803:G:A 1/140220) Row 485803416 (NC_000016.10:23640803:G:C 2/140220) Row 485803417 (NC_000016.10:23640803:G:T 759/140220)	-	Apr 26, 2021 (155)
31	gnomAD - Genomes Submission ignored due to conflicting rows: Row 485803415 (NC_000016.10:23640803:G:A 1/140220) Row 485803416 (NC_000016.10:23640803:G:C 2/140220) Row 485803417 (NC_000016.10:23640803:G:T 759/140220)	-	Apr 26, 2021 (155)
32	Genome of the Netherlands Release 5	NC_000016.9 - 23652125	Apr 27, 2020 (154)
33	Northern Sweden	NC_000016.9 - 23652125	Jul 13, 2019 (153)
34	Qatari	NC_000016.9 - 23652125	Apr 27, 2020 (154)
35	SGDP_PRJ	NC_000016.9 - 23652125	Apr 27, 2020 (154)
36	TopMed Submission ignored due to conflicting rows: Row 226667623 (NC_000016.10:23640803:G:A 3/264690) Row 226667624 (NC_000016.10:23640803:G:C 7/264690) Row 226667625 (NC_000016.10:23640803:G:T 1343/264690)	-	Apr 26, 2021 (155)
37	TopMed Submission ignored due to conflicting rows: Row 226667623 (NC_000016.10:23640803:G:A 3/264690) Row 226667624 (NC_000016.10:23640803:G:C 7/264690) Row 226667625 (NC_000016.10:23640803:G:T 1343/264690)	-	Apr 26, 2021 (155)
38	TopMed Submission ignored due to conflicting rows: Row 226667623 (NC_000016.10:23640803:G:A 3/264690) Row 226667624 (NC_000016.10:23640803:G:C 7/264690) Row 226667625 (NC_000016.10:23640803:G:T 1343/264690)	-	Apr 26, 2021 (155)
39	UK 10K study - Twins	NC_000016.9 - 23652125	Oct 12, 2018 (152)
40	ALFA	NC_000016.10 - 23640804	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
1566166418, ss5011121962	NC_000016.10:23640803:G:A	NC_000016.10:23640803:G:A	(self)
1566166418, ss5011121963	NC_000016.10:23640803:G:C	NC_000016.10:23640803:G:C	(self)
68927413, 38260004, 27072218, 17067599, 14707429, 17847623, 36190205, 38260004, ss339180196, ss992382825, ss1355779408, ss1634205674, ss1677199707, ss1935805701, ss2941513356, ss3014246709, ss3681333970, ss3741422564, ss3884173225, ss5422951686, ss5658668760, ss5846244225, ss5950086425	NC_000016.9:23652124:G:T	NC_000016.10:23640803:G:T	(self)
90434989, 1566166418, ss2211355777, ss3699034871, ss5011121964, ss5300504262, ss5493957086, ss5602909054, ss5898656194	NC_000016.10:23640803:G:T	NC_000016.10:23640803:G: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 rs142098064

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs142098064