rs12492170

Variant names:

• chr3-137157977-G-A
• rs12492170

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 0.196 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.149 AC: 6172 AN: 41514

American (AMR) AF: 0.232 AC: 3539 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2031 AN: 5172

South Asian (SAS) AF: 0.207 AC: 997 AN: 4824

European-Finnish (FIN) AF: 0.284 AC: 3001 AN: 10558

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12986 AN: 68006

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.183 Hom.: 343

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12492170; hg19: chr3-136876819;