3-46353189-A-T

Variant names:

• chr3-46353189-A-T
• rs3918359

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 0.8 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.800 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

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.765

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3918359; hg19: chr3-46394680;