rs72760840

Variant names:

• chr16-3901739-T-A
• rs72760840

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 0.362 in 151,948 control chromosomes in the GnomAD database, including 10,551 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 0.36 (10551 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 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: 0.363 AC: 55059 AN: 151830 Hom.: 10559 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.362 AC: 55053 AN: 151948 Hom.: 10551 Cov.: 31 AF XY: 0.357 AC XY: 26533 AN XY: 74264

African (AFR) AF: 0.299 AC: 12419 AN: 41466

American (AMR) AF: 0.331 AC: 5033 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3464

East Asian (EAS) AF: 0.0528 AC: 272 AN: 5154

South Asian (SAS) AF: 0.203 AC: 980 AN: 4818

European-Finnish (FIN) AF: 0.415 AC: 4382 AN: 10562

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28960 AN: 67946

Other (OTH) AF: 0.361 AC: 760 AN: 2108

Alfa AF: 0.402 Hom.: 1579

Bravo AF: 0.356

Asia WGS AF: 0.143 AC: 498 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.42
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs72760840; hg19: chr16-3951740;