rs3764628

chr19-18636795-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.101 in 149,956 control chromosomes in the GnomAD database, including 926 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 0.10 (926 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15073 AN: 149838 Hom.: 927 Cov.: 30

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0683

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.101 AC: 15074 AN: 149956 Hom.: 926 Cov.: 30 AF XY: 0.0996 AC XY: 7290 AN XY: 73208

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.0927

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.105

Alfa AF: 0.129 Hom.: 2892

Bravo AF: 0.0942

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.6
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3764628; hg19: chr19-18747605;