chr16-62638708-G-A

Variant names:

• chr16-62638708-G-A
• rs288604

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 0.87 in 152,240 control chromosomes in the GnomAD database, including 57,732 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 0.87 (57732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 3 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 = 0.976 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: 0.870 AC: 132373 AN: 152122 Hom.: 57681 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.870 AC: 132482 AN: 152240 Hom.: 57732 Cov.: 32 AF XY: 0.875 AC XY: 65117 AN XY: 74448

African (AFR) AF: 0.825 AC: 34242 AN: 41518

American (AMR) AF: 0.899 AC: 13749 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5170 AN: 5176

South Asian (SAS) AF: 0.969 AC: 4681 AN: 4830

European-Finnish (FIN) AF: 0.899 AC: 9537 AN: 10612

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59177 AN: 68018

Other (OTH) AF: 0.871 AC: 1842 AN: 2116

Alfa AF: 0.873 Hom.: 42805

Bravo AF: 0.867

Asia WGS AF: 0.973 AC: 3386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.38
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs288604; hg19: chr16-62672612;