chr3-46353189-A-T

Variant names:

• chr3-46353189-A-T
• rs3918359

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 0.8 in 151,630 control chromosomes in the GnomAD database, including 48,904 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 0.80 (48904 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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: 0.800 AC: 121191 AN: 151512 Hom.: 48844 Cov.: 27

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.800 AC: 121306 AN: 151630 Hom.: 48904 Cov.: 27 AF XY: 0.801 AC XY: 59357 AN XY: 74076

African (AFR) AF: 0.896 AC: 36996 AN: 41276

American (AMR) AF: 0.708 AC: 10773 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2737 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3711 AN: 5146

South Asian (SAS) AF: 0.843 AC: 4041 AN: 4794

European-Finnish (FIN) AF: 0.848 AC: 8906 AN: 10506

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51574 AN: 67930

Other (OTH) AF: 0.765 AC: 1607 AN: 2100

Alfa AF: 0.799 Hom.: 5687

Bravo AF: 0.794

Asia WGS AF: 0.799 AC: 2781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3918359; hg19: chr3-46394680;