rs3760469

Variant names:

• chr17-51153191-T-G
• rs3760469

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 0.547 in 152,090 control chromosomes in the GnomAD database, including 23,493 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 0.55 (23493 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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: 0.547 AC: 83096 AN: 151972 Hom.: 23464 Cov.: 33

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.547 AC: 83177 AN: 152090 Hom.: 23493 Cov.: 33 AF XY: 0.540 AC XY: 40179 AN XY: 74350

African (AFR) AF: 0.693 AC: 28767 AN: 41484

American (AMR) AF: 0.510 AC: 7779 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2064 AN: 5188

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4826

European-Finnish (FIN) AF: 0.487 AC: 5138 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34325 AN: 67996

Other (OTH) AF: 0.531 AC: 1122 AN: 2114

Alfa AF: 0.508 Hom.: 20776

Bravo AF: 0.559

Asia WGS AF: 0.416 AC: 1445 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	1.3
DANN	Benign	0.57
PhyloP100		-0.40
PromoterAI		-0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760469; hg19: chr17-49230552;