rs3760687

Variant names:

• chr19-7702508-C-T
• rs3760687

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 0.0536 in 152,150 control chromosomes in the GnomAD database, including 309 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 0.054 (309 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0535 AC: 8139 AN: 152032 Hom.: 307 Cov.: 30

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0536 AC: 8156 AN: 152150 Hom.: 309 Cov.: 30 AF XY: 0.0569 AC XY: 4235 AN XY: 74370

African (AFR) AF: 0.0640 AC: 2658 AN: 41504

American (AMR) AF: 0.0674 AC: 1029 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3468

East Asian (EAS) AF: 0.181 AC: 933 AN: 5156

South Asian (SAS) AF: 0.0822 AC: 397 AN: 4830

European-Finnish (FIN) AF: 0.0581 AC: 615 AN: 10594

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0349 AC: 2375 AN: 68018

Other (OTH) AF: 0.0416 AC: 88 AN: 2114

Alfa AF: 0.0395 Hom.: 281

Bravo AF: 0.0541

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.32
PhyloP100		-1.4
PromoterAI		0.034	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760687; hg19: chr19-7767394;