rs16862537

chr3-187746184-T-C

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 0.2 in 151,962 control chromosomes in the GnomAD database, including 3,782 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 (3782 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.201 AC: 30453 AN: 151842 Hom.: 3785 Cov.: 31

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.200 AC: 30438 AN: 151962 Hom.: 3782 Cov.: 31 AF XY: 0.197 AC XY: 14613 AN XY: 74274

Gnomad4 AFR AF: 0.0585

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.228

Alfa AF: 0.206 Hom.: 546

Bravo AF: 0.196

Asia WGS AF: 0.206 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	14
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16862537; hg19: chr3-187463972; COSMIC: COSV69206459;