2-631528-A-G

Variant names:

• chr2-631528-A-G
• rs7585056

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 0.852 in 151,934 control chromosomes in the GnomAD database, including 55,297 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 0.85 (55297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.852 AC: 129390 AN: 151808 Hom.: 55250 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.837

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.852 AC: 129498 AN: 151934 Hom.: 55297 Cov.: 32 AF XY: 0.855 AC XY: 63482 AN XY: 74260

African (AFR) AF: 0.887 AC: 36843 AN: 41520

American (AMR) AF: 0.871 AC: 13298 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2579 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4757 AN: 5178

South Asian (SAS) AF: 0.860 AC: 4144 AN: 4816

European-Finnish (FIN) AF: 0.849 AC: 8976 AN: 10572

Middle Eastern (MID) AF: 0.826 AC: 233 AN: 282

European-Non Finnish (NFE) AF: 0.828 AC: 56169 AN: 67804

Other (OTH) AF: 0.845 AC: 1781 AN: 2108

Alfa AF: 0.857 Hom.: 16942

Bravo AF: 0.854

Asia WGS AF: 0.893 AC: 3071 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7585056; hg19: chr2-631528;