rs4931122

Variant names:

• chr12-28948087-A-G
• rs4931122

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.560

Alfa AF: 0.585 Hom.: 4453

Bravo AF: 0.565

Asia WGS AF: 0.558 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4931122; hg19: chr12-29101020;