rs251633

Variant names:

• chr16-15386022-G-T
• rs251633

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 0.188 in 152,014 control chromosomes in the GnomAD database, including 3,436 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 0.19 (3436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.188 AC: 28611 AN: 151896 Hom.: 3429 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0683

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.188 AC: 28628 AN: 152014 Hom.: 3436 Cov.: 32 AF XY: 0.198 AC XY: 14727 AN XY: 74310

African (AFR) AF: 0.110 AC: 4569 AN: 41494

American (AMR) AF: 0.283 AC: 4325 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2771 AN: 5164

South Asian (SAS) AF: 0.227 AC: 1093 AN: 4822

European-Finnish (FIN) AF: 0.284 AC: 2991 AN: 10522

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11721 AN: 67966

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.179 Hom.: 1966

Bravo AF: 0.187

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.18
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs251633; hg19: chr16-15479879;