rs2764743

Variant names:

• chr16-20019883-T-A
• rs2764743

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 0.112 in 152,044 control chromosomes in the GnomAD database, including 1,690 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 0.11 (1690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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: 0.112 AC: 17015 AN: 151926 Hom.: 1685 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.112 AC: 17035 AN: 152044 Hom.: 1690 Cov.: 32 AF XY: 0.111 AC XY: 8231 AN XY: 74324

African (AFR) AF: 0.258 AC: 10685 AN: 41418

American (AMR) AF: 0.102 AC: 1557 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3468

East Asian (EAS) AF: 0.126 AC: 650 AN: 5148

South Asian (SAS) AF: 0.109 AC: 524 AN: 4816

European-Finnish (FIN) AF: 0.0302 AC: 320 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2628 AN: 68008

Other (OTH) AF: 0.0900 AC: 190 AN: 2110

Alfa AF: 0.0792 Hom.: 114

Bravo AF: 0.125

Asia WGS AF: 0.118 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.017
DANN	Benign	0.089
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2764743; hg19: chr16-20031205;