chr3-162413620-T-C

Variant names:

• chr3-162413620-T-C
• rs12636148

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 0.104 in 150,364 control chromosomes in the GnomAD database, including 1,630 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 0.10 (1630 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.104 AC: 15636 AN: 150246 Hom.: 1623 Cov.: 31

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0805

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.0645

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.104 AC: 15643 AN: 150364 Hom.: 1630 Cov.: 31 AF XY: 0.107 AC XY: 7878 AN XY: 73410

African (AFR) AF: 0.0309 AC: 1276 AN: 41328

American (AMR) AF: 0.219 AC: 3271 AN: 14966

Ashkenazi Jewish (ASJ) AF: 0.0805 AC: 276 AN: 3428

East Asian (EAS) AF: 0.242 AC: 1242 AN: 5140

South Asian (SAS) AF: 0.174 AC: 829 AN: 4770

European-Finnish (FIN) AF: 0.0992 AC: 1015 AN: 10228

Middle Eastern (MID) AF: 0.0734 AC: 21 AN: 286

European-Non Finnish (NFE) AF: 0.109 AC: 7362 AN: 67252

Other (OTH) AF: 0.124 AC: 256 AN: 2070

Alfa AF: 0.106 Hom.: 3002

Bravo AF: 0.114

Asia WGS AF: 0.152 AC: 524 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.81
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs12636148; hg19: chr3-162131408;