3-46350569-C-T

Variant names:

• chr3-46350569-C-T
• rs17141010

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 0.132 in 152,116 control chromosomes in the GnomAD database, including 1,570 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 0.13 (1570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 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: 0.132 AC: 20086 AN: 151998 Hom.: 1563 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0634

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.132 AC: 20121 AN: 152116 Hom.: 1570 Cov.: 32 AF XY: 0.133 AC XY: 9896 AN XY: 74370

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0634

Gnomad4 NFE AF: 0.0902

Gnomad4 OTH AF: 0.136

Alfa AF: 0.131 Hom.: 212

Bravo AF: 0.145

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.55
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17141010; hg19: chr3-46392060;