3-46350569-C-T

Variant names:

• chr3-46350569-C-T
• rs17141010

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 0.132 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.195 AC: 8076 AN: 41470

American (AMR) AF: 0.175 AC: 2683 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1097 AN: 5176

South Asian (SAS) AF: 0.121 AC: 581 AN: 4818

European-Finnish (FIN) AF: 0.0634 AC: 672 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0902 AC: 6132 AN: 67980

Other (OTH) AF: 0.136 AC: 288 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.55
DANN	Benign	0.47
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17141010; hg19: chr3-46392060;