16-31102913-A-G

Position:

• chr16-31102913-A-G

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 0.569 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.537

Alfa AF: 0.512 Hom.: 1695

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61162043; hg19: chr16-31114234;