rs946263

Variant names:

• chr1-203196253-G-A
• rs946263

Your query was ambiguous. Multiple possible variants found:

• chr1-203196253-G-A
• chr1-203196253-G-C
• chr1-203196253-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.866 in 152,228 control chromosomes in the GnomAD database, including 57,371 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.87 (57371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131741 AN: 152112 Hom.: 57316 Cov.: 32

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.879

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.866 AC: 131853 AN: 152228 Hom.: 57371 Cov.: 32 AF XY: 0.868 AC XY: 64575 AN XY: 74402

African (AFR) AF: 0.934 AC: 38803 AN: 41534

American (AMR) AF: 0.911 AC: 13951 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3172 AN: 3472

East Asian (EAS) AF: 0.963 AC: 4986 AN: 5178

South Asian (SAS) AF: 0.891 AC: 4303 AN: 4828

European-Finnish (FIN) AF: 0.783 AC: 8291 AN: 10584

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55379 AN: 68006

Other (OTH) AF: 0.879 AC: 1859 AN: 2114

Alfa AF: 0.842 Hom.: 109846

Bravo AF: 0.880

Asia WGS AF: 0.916 AC: 3181 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.057
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs946263; hg19: chr1-203165381;