rs3760657

Variant names:

• chr19-40989528-A-G
• rs3760657

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 0.093 in 152,198 control chromosomes in the GnomAD database, including 880 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 0.093 (880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 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: 0.0930 AC: 14140 AN: 152080 Hom.: 875 Cov.: 32

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0930 AC: 14150 AN: 152198 Hom.: 880 Cov.: 32 AF XY: 0.0979 AC XY: 7284 AN XY: 74414

African (AFR) AF: 0.0417 AC: 1732 AN: 41512

American (AMR) AF: 0.153 AC: 2336 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3472

East Asian (EAS) AF: 0.171 AC: 886 AN: 5180

South Asian (SAS) AF: 0.137 AC: 660 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1594 AN: 10596

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0938 AC: 6381 AN: 68012

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0944 Hom.: 1291

Bravo AF: 0.0918

Asia WGS AF: 0.144 AC: 498 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.63
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs3760657; hg19: chr19-41495433;