rs3181157

chr12-6199357-C-T

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 0.179 in 149,966 control chromosomes in the GnomAD database, including 3,664 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 0.18 (3664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 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: 0.179 AC: 26757 AN: 149846 Hom.: 3654 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.110

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.179 AC: 26801 AN: 149966 Hom.: 3664 Cov.: 32 AF XY: 0.177 AC XY: 12929 AN XY: 73164

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0521

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0893

Gnomad4 NFE AF: 0.0920

Gnomad4 OTH AF: 0.148

Alfa AF: 0.102 Hom.: 1449

Bravo AF: 0.188

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181157; hg19: chr12-6308523;