16-82176256-A-G

Variant names:

• chr16-82176256-A-G
• rs2967374

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 0.844 in 152,218 control chromosomes in the GnomAD database, including 54,610 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 0.84 (54610 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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: 0.844 AC: 128367 AN: 152100 Hom.: 54553 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.844 AC: 128482 AN: 152218 Hom.: 54610 Cov.: 32 AF XY: 0.849 AC XY: 63143 AN XY: 74412

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.822

Alfa AF: 0.768 Hom.: 2674

Bravo AF: 0.847

Asia WGS AF: 0.847 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2967374; hg19: chr16-82209861;