rs12492170

chr3-137157977-G-A

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 0.196 in 152,136 control chromosomes in the GnomAD database, including 3,265 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 0.20 (3265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.197 AC: 29875 AN: 152018 Hom.: 3269 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.196 AC: 29885 AN: 152136 Hom.: 3265 Cov.: 32 AF XY: 0.204 AC XY: 15174 AN XY: 74362

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.193

Alfa AF: 0.185 Hom.: 338

Bravo AF: 0.191

Asia WGS AF: 0.311 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12492170; hg19: chr3-136876819;