rs4931122

Variant names:

• chr12-28948087-A-G
• rs4931122

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 0.565 in 151,618 control chromosomes in the GnomAD database, including 24,695 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 0.57 (24695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.664 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: 0.565 AC: 85667 AN: 151500 Hom.: 24686 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.565 AC: 85696 AN: 151618 Hom.: 24695 Cov.: 32 AF XY: 0.572 AC XY: 42376 AN XY: 74046

African (AFR) AF: 0.478 AC: 19792 AN: 41374

American (AMR) AF: 0.675 AC: 10282 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1921 AN: 3456

East Asian (EAS) AF: 0.485 AC: 2471 AN: 5098

South Asian (SAS) AF: 0.657 AC: 3167 AN: 4818

European-Finnish (FIN) AF: 0.641 AC: 6773 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39432 AN: 67762

Other (OTH) AF: 0.560 AC: 1181 AN: 2110

Alfa AF: 0.582 Hom.: 4547

Bravo AF: 0.565

Asia WGS AF: 0.558 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.9
DANN	Benign	0.83
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs4931122; hg19: chr12-29101020;