3-166431104-C-T

Position:

• chr3-166431104-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 0.171 in 151,728 control chromosomes in the GnomAD database, including 2,218 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 0.17 (2218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 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: 0.171 AC: 25890 AN: 151610 Hom.: 2211 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.171 AC: 25908 AN: 151728 Hom.: 2218 Cov.: 32 AF XY: 0.172 AC XY: 12745 AN XY: 74148

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.195

Alfa AF: 0.161 Hom.: 2772

Bravo AF: 0.174

Asia WGS AF: 0.104 AC: 361 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.2
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2863389; hg19: chr3-166148892;