rs3746166

Variant names:

• chr19-1102176-C-T
• rs3746166

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 0.536 in 151,912 control chromosomes in the GnomAD database, including 21,977 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 0.54 (21977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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: 0.536 AC: 81379 AN: 151794 Hom.: 21941 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.536 AC: 81470 AN: 151912 Hom.: 21977 Cov.: 32 AF XY: 0.544 AC XY: 40407 AN XY: 74252

African (AFR) AF: 0.593 AC: 24556 AN: 41404

American (AMR) AF: 0.586 AC: 8947 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3468

East Asian (EAS) AF: 0.548 AC: 2828 AN: 5164

South Asian (SAS) AF: 0.551 AC: 2656 AN: 4822

European-Finnish (FIN) AF: 0.609 AC: 6420 AN: 10550

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32515 AN: 67930

Other (OTH) AF: 0.521 AC: 1094 AN: 2098

Alfa AF: 0.533 Hom.: 2825

Bravo AF: 0.534

Asia WGS AF: 0.581 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.36
DANN	Benign	0.54
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs3746166; hg19: chr19-1102175;