rs1167125

chr12-43040479-C-Achr12-43040479-C-G

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 0.938 in 152,148 control chromosomes in the GnomAD database, including 67,035 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 0.94 (67035 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142643 AN: 152030 Hom.: 66986 Cov.: 31

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.938 AC: 142750 AN: 152148 Hom.: 67035 Cov.: 31 AF XY: 0.940 AC XY: 69936 AN XY: 74380

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.929

Alfa AF: 0.938 Hom.: 85988

Bravo AF: 0.934

Asia WGS AF: 0.941 AC: 3254 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.1
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1167125; hg19: chr12-43434282; COSMIC: COSV62490409;