rs3746166

Positions:

• chr19-1102176-C-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 0.536 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.521

Alfa AF: 0.530 Hom.: 2669

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3746166; hg19: chr19-1102175;