16-31511792-A-G

Variant names:

• chr16-31511792-A-G
• rs7187900

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 0.57 in 152,064 control chromosomes in the GnomAD database, including 25,950 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 0.57 (25950 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.931
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 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: 0.569 AC: 86478 AN: 151944 Hom.: 25887 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.570 AC: 86601 AN: 152064 Hom.: 25950 Cov.: 33 AF XY: 0.569 AC XY: 42256 AN XY: 74324

African (AFR) AF: 0.752 AC: 31189 AN: 41466

American (AMR) AF: 0.444 AC: 6782 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3472

East Asian (EAS) AF: 0.360 AC: 1860 AN: 5168

South Asian (SAS) AF: 0.769 AC: 3715 AN: 4828

European-Finnish (FIN) AF: 0.486 AC: 5134 AN: 10564

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34395 AN: 67974

Other (OTH) AF: 0.509 AC: 1075 AN: 2110

Alfa AF: 0.518 Hom.: 58043

Bravo AF: 0.563

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.73
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs7187900; hg19: chr16-31523113;