16-31102913-A-G

Variant names:

• chr16-31102913-A-G
• rs61162043

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 0.569 in 150,576 control chromosomes in the GnomAD database, including 25,340 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 (25340 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 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: 0.568 AC: 85519 AN: 150460 Hom.: 25309 Cov.: 26

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.569 AC: 85603 AN: 150576 Hom.: 25340 Cov.: 26 AF XY: 0.570 AC XY: 41901 AN XY: 73502

African (AFR) AF: 0.499 AC: 20387 AN: 40818

American (AMR) AF: 0.573 AC: 8648 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1578 AN: 3456

East Asian (EAS) AF: 0.108 AC: 554 AN: 5130

South Asian (SAS) AF: 0.817 AC: 3906 AN: 4782

European-Finnish (FIN) AF: 0.609 AC: 6276 AN: 10308

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.628 AC: 42539 AN: 67708

Other (OTH) AF: 0.537 AC: 1116 AN: 2080

Alfa AF: 0.789 Hom.: 8342

Bravo AF: 0.548

Asia WGS AF: 0.514 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs61162043; hg19: chr16-31114234;