rs1981760

Variant names:

• chr16-50689163-C-T
• rs1981760

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 0.672 in 152,152 control chromosomes in the GnomAD database, including 35,384 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 0.67 (35384 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 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: 0.672 AC: 102135 AN: 152034 Hom.: 35368 Cov.: 34

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.672 AC: 102198 AN: 152152 Hom.: 35384 Cov.: 34 AF XY: 0.663 AC XY: 49308 AN XY: 74374

African (AFR) AF: 0.645 AC: 26759 AN: 41480

American (AMR) AF: 0.616 AC: 9424 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2857 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1312 AN: 5180

South Asian (SAS) AF: 0.365 AC: 1761 AN: 4826

European-Finnish (FIN) AF: 0.707 AC: 7472 AN: 10572

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50309 AN: 68016

Other (OTH) AF: 0.668 AC: 1413 AN: 2114

Alfa AF: 0.711 Hom.: 90632

Bravo AF: 0.664

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.73
DANN	Benign	0.41
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1981760; hg19: chr16-50723074;