rs3918357

Variant names:

• chr3-46352479-C-A
• rs3918357

Your query was ambiguous. Multiple possible variants found:

• chr3-46352479-C-A
• chr3-46352479-C-T

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 152,090 control chromosomes in the GnomAD database, including 1,568 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 (1568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

Selected	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: 20098 AN: 151972 Hom.: 1561 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0634

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0901

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: 20133 AN: 152090 Hom.: 1568 Cov.: 32 AF XY: 0.133 AC XY: 9913 AN XY: 74372

African (AFR) AF: 0.195 AC: 8091 AN: 41464

American (AMR) AF: 0.176 AC: 2684 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1093 AN: 5170

South Asian (SAS) AF: 0.122 AC: 588 AN: 4808

European-Finnish (FIN) AF: 0.0634 AC: 672 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0901 AC: 6125 AN: 67984

Other (OTH) AF: 0.137 AC: 288 AN: 2108

Alfa AF: 0.0553 Hom.: 61

Bravo AF: 0.145

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.68
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs3918357; hg19: chr3-46393970;