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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.

rs148560784

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:14844966 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000128 (34/264690, TOPMED)
T=0.000056 (10/178460, GnomAD_exome)
T=0.000086 (9/104507, GnomAD) (+ 5 more)
T=0.00007 (6/86016, ExAC)
T=0.00017 (4/23028, ALFA)
T=0.00004 (1/22223, 14KJPN)
T=0.00008 (1/12843, 8.3KJPN)
T=0.00019 (2/10562, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
FANCB : Missense 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 23028 C=0.99983 T=0.00017
European Sub 15744 C=0.99975 T=0.00025
African Sub 3492 C=1.0000 T=0.0000
African Others Sub 122 C=1.000 T=0.000
African American Sub 3370 C=1.0000 T=0.0000
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 2770 C=1.0000 T=0.0000


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
TopMed Global Study-wide 264690 C=0.999872 T=0.000128
gnomAD - Exomes Global Study-wide 178460 C=0.999944 T=0.000056
gnomAD - Exomes European Sub 95752 C=0.99991 T=0.00009
gnomAD - Exomes Asian Sub 31340 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 26871 C=0.99996 T=0.00004
gnomAD - Exomes African Sub 13111 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 7000 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 4386 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 104507 C=0.999914 T=0.000086
gnomAD - Genomes European Sub 57275 C=0.99984 T=0.00016
gnomAD - Genomes African Sub 31460 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 9423 C=1.0000 T=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2527 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 2254 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1568 C=1.0000 T=0.0000
ExAC Global Study-wide 86016 C=0.99993 T=0.00007
ExAC Europe Sub 52097 C=0.99988 T=0.00012
ExAC Asian Sub 15506 C=1.00000 T=0.00000
ExAC American Sub 9305 C=1.0000 T=0.0000
ExAC African Sub 8492 C=1.0000 T=0.0000
ExAC Other Sub 616 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 23028 C=0.99983 T=0.00017
Allele Frequency Aggregator European Sub 15744 C=0.99975 T=0.00025
Allele Frequency Aggregator African Sub 3492 C=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 2770 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
14KJPN JAPANESE Study-wide 22223 C=0.99996 T=0.00004
8.3KJPN JAPANESE Study-wide 12843 C=0.99992 T=0.00008
GO Exome Sequencing Project Global Study-wide 10562 C=0.99981 T=0.00019
GO Exome Sequencing Project European American Sub 6727 C=0.9997 T=0.0003
GO Exome Sequencing Project African American Sub 3835 C=1.0000 T=0.0000
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.p14 chr X NC_000023.11:g.14844966C>T
GRCh37.p13 chr X NC_000023.10:g.14863088C>T
FANCB RefSeqGene (LRG_496) NG_007310.1:g.33097G>A
Gene: FANCB, FA complementation group B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FANCB transcript variant 1 NM_001018113.3:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform 1 NP_001018123.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant 2 NM_152633.4:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform 1 NP_689846.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant 3 NM_001324162.2:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform 1 NP_001311091.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant 4 NR_136707.2:n. N/A Genic Downstream Transcript Variant
FANCB transcript variant X2 XM_011545470.3:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform X1 XP_011543772.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant X5 XM_047441920.1:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform X1 XP_047297876.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant X6 XM_047441921.1:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform X1 XP_047297877.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant X7 XM_017029356.2:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform X2 XP_016884845.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant X8 XM_047441922.1:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform X2 XP_047297878.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant X9 XM_047441923.1:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform X2 XP_047297879.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant X10 XM_047441924.1:c.1817G>A S [AGT] > N [AAT] Coding Sequence Variant
Fanconi anemia group B protein isoform X2 XP_047297880.1:p.Ser606Asn S (Ser) > N (Asn) Missense Variant
FANCB transcript variant X4 XR_001755672.2:n.2092G>A N/A Non Coding Transcript Variant
FANCB transcript variant X1 XR_007068184.1:n.2071G>A N/A Non Coding Transcript Variant
FANCB transcript variant X2 XR_001755673.2:n.6034G>A N/A Non Coding Transcript Variant
FANCB transcript variant X3 XR_001755674.2:n.1971G>A N/A Non Coding Transcript 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.

Allele: T (allele ID: 338985 )
ClinVar Accession Disease Names Clinical Significance
RCV000260730.3 VACTERL association, X-linked, with or without hydrocephalus Likely-Benign
RCV000318403.3 Fanconi anemia complementation group B Likely-Benign
RCV001404085.4 Fanconi anemia Likely-Benign
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 C= T
GRCh38.p14 chr X NC_000023.11:g.14844966= NC_000023.11:g.14844966C>T
GRCh37.p13 chr X NC_000023.10:g.14863088= NC_000023.10:g.14863088C>T
FANCB RefSeqGene (LRG_496) NG_007310.1:g.33097= NG_007310.1:g.33097G>A
FANCB transcript variant 2 NM_152633.4:c.1817= NM_152633.4:c.1817G>A
FANCB transcript variant 2 NM_152633.3:c.1817= NM_152633.3:c.1817G>A
FANCB transcript variant 2 NM_152633.2:c.1817= NM_152633.2:c.1817G>A
FANCB transcript variant 1 NM_001018113.3:c.1817= NM_001018113.3:c.1817G>A
FANCB transcript variant 1 NM_001018113.2:c.1817= NM_001018113.2:c.1817G>A
FANCB transcript variant 1 NM_001018113.1:c.1817= NM_001018113.1:c.1817G>A
FANCB transcript variant 3 NM_001324162.2:c.1817= NM_001324162.2:c.1817G>A
FANCB transcript variant 3 NM_001324162.1:c.1817= NM_001324162.1:c.1817G>A
FANCB transcript variant 5 NM_001410764.1:c.1817= NM_001410764.1:c.1817G>A
FANCB transcript variant X2 XM_011545470.3:c.1817= XM_011545470.3:c.1817G>A
FANCB transcript variant X2 XR_001755673.2:n.6034= XR_001755673.2:n.6034G>A
FANCB transcript variant X3 XR_001755673.1:n.2070= XR_001755673.1:n.2070G>A
FANCB transcript variant X4 XR_001755672.2:n.2092= XR_001755672.2:n.2092G>A
FANCB transcript variant X1 XR_001755672.1:n.2278= XR_001755672.1:n.2278G>A
FANCB transcript variant X3 XR_001755674.2:n.1971= XR_001755674.2:n.1971G>A
FANCB transcript variant X4 XR_001755674.1:n.1971= XR_001755674.1:n.1971G>A
FANCB transcript variant X7 XM_017029356.2:c.1817= XM_017029356.2:c.1817G>A
FANCB transcript variant X6 XM_017029356.1:c.1817= XM_017029356.1:c.1817G>A
FANCB transcript variant X10 XM_047441924.1:c.1817= XM_047441924.1:c.1817G>A
FANCB transcript variant X5 XM_047441920.1:c.1817= XM_047441920.1:c.1817G>A
FANCB transcript variant X6 XM_047441921.1:c.1817= XM_047441921.1:c.1817G>A
FANCB transcript variant X1 XR_007068184.1:n.2071= XR_007068184.1:n.2071G>A
FANCB transcript variant X8 XM_047441922.1:c.1817= XM_047441922.1:c.1817G>A
FANCB transcript variant X9 XM_047441923.1:c.1817= XM_047441923.1:c.1817G>A
Fanconi anemia group B protein isoform 1 NP_689846.1:p.Ser606= NP_689846.1:p.Ser606Asn
Fanconi anemia group B protein isoform 1 NP_001018123.1:p.Ser606= NP_001018123.1:p.Ser606Asn
Fanconi anemia group B protein isoform 1 NP_001311091.1:p.Ser606= NP_001311091.1:p.Ser606Asn
Fanconi anemia group B protein isoform X1 XP_011543772.1:p.Ser606= XP_011543772.1:p.Ser606Asn
Fanconi anemia group B protein isoform X2 XP_016884845.1:p.Ser606= XP_016884845.1:p.Ser606Asn
Fanconi anemia group B protein isoform X2 XP_047297880.1:p.Ser606= XP_047297880.1:p.Ser606Asn
Fanconi anemia group B protein isoform X1 XP_047297876.1:p.Ser606= XP_047297876.1:p.Ser606Asn
Fanconi anemia group B protein isoform X1 XP_047297877.1:p.Ser606= XP_047297877.1:p.Ser606Asn
Fanconi anemia group B protein isoform X2 XP_047297878.1:p.Ser606= XP_047297878.1:p.Ser606Asn
Fanconi anemia group B protein isoform X2 XP_047297879.1:p.Ser606= XP_047297879.1:p.Ser606Asn
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#.

11 SubSNP, 8 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342549988 May 09, 2011 (134)
2 EVA_EXAC ss1694461654 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2315857075 Dec 20, 2016 (150)
4 GNOMAD ss2745312681 Nov 08, 2017 (151)
5 GNOMAD ss2746079316 Nov 08, 2017 (151)
6 GNOMAD ss2976735181 Nov 08, 2017 (151)
7 EVA ss3825473586 Apr 27, 2020 (154)
8 TOPMED ss5116241568 Apr 27, 2021 (155)
9 TOMMO_GENOMICS ss5233638456 Apr 27, 2021 (155)
10 HUGCELL_USP ss5503620462 Oct 16, 2022 (156)
11 TOMMO_GENOMICS ss5795097722 Oct 16, 2022 (156)
12 ExAC NC_000023.10 - 14863088 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000023.11 - 14844966 Apr 27, 2021 (155)
14 gnomAD - Exomes NC_000023.10 - 14863088 Jul 13, 2019 (153)
15 GO Exome Sequencing Project NC_000023.10 - 14863088 Oct 12, 2018 (152)
16 8.3KJPN NC_000023.10 - 14863088 Apr 27, 2021 (155)
17 14KJPN NC_000023.11 - 14844966 Oct 16, 2022 (156)
18 TopMed NC_000023.11 - 14844966 Apr 27, 2021 (155)
19 ALFA NC_000023.11 - 14844966 Apr 27, 2021 (155)
20 ClinVar RCV000260730.3 Oct 16, 2022 (156)
21 ClinVar RCV000318403.3 Oct 16, 2022 (156)
22 ClinVar RCV001404085.4 Oct 16, 2022 (156)
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
9959063, 14649200, 1930390, 91607763, ss342549988, ss1694461654, ss2745312681, ss2746079316, ss2976735181, ss3825473586, ss5233638456 NC_000023.10:14863087:C:T NC_000023.11:14844965:C:T (self)
RCV000260730.3, RCV000318403.3, RCV001404085.4, 575771221, 128934826, 679847925, 13878142245, ss2315857075, ss5116241568, ss5503620462, ss5795097722 NC_000023.11:14844965:C:T NC_000023.11:14844965:C:T (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 rs148560784

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.post761+d5e8e07