rs7561317

Variant names:

• chr2-644953-A-G
• rs7561317

Your query was ambiguous. Multiple possible variants found:

• chr2-644953-A-G
• chr2-644953-A-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 0.817 in 152,184 control chromosomes in the GnomAD database, including 50,952 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 0.82 (50952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 104 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124264 AN: 152066 Hom.: 50931 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.817 AC: 124340 AN: 152184 Hom.: 50952 Cov.: 33 AF XY: 0.821 AC XY: 61067 AN XY: 74422

African (AFR) AF: 0.767 AC: 31807 AN: 41478

American (AMR) AF: 0.857 AC: 13112 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2549 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4751 AN: 5172

South Asian (SAS) AF: 0.860 AC: 4144 AN: 4820

European-Finnish (FIN) AF: 0.849 AC: 9003 AN: 10608

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56272 AN: 68016

Other (OTH) AF: 0.827 AC: 1744 AN: 2110

Alfa AF: 0.823 Hom.: 191424

Bravo AF: 0.814

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7561317; hg19: chr2-644953;