chr2-629244-A-C

Variant names:

• chr2-629244-A-C
• rs12463617

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 0.818 in 152,190 control chromosomes in the GnomAD database, including 51,085 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 (51085 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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: 0.818 AC: 124421 AN: 152072 Hom.: 51058 Cov.: 34

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.818 AC: 124505 AN: 152190 Hom.: 51085 Cov.: 34 AF XY: 0.822 AC XY: 61148 AN XY: 74410

African (AFR) AF: 0.768 AC: 31868 AN: 41506

American (AMR) AF: 0.859 AC: 13139 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2590 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4749 AN: 5168

South Asian (SAS) AF: 0.851 AC: 4105 AN: 4826

European-Finnish (FIN) AF: 0.849 AC: 8992 AN: 10588

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56370 AN: 68016

Other (OTH) AF: 0.821 AC: 1733 AN: 2110

Alfa AF: 0.822 Hom.: 75382

Bravo AF: 0.815

Asia WGS AF: 0.881 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.78
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12463617; hg19: chr2-629244;