3-46295290-G-A

Variant names:

• chr3-46295290-G-A
• rs7645716

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 0.274 in 151,942 control chromosomes in the GnomAD database, including 6,169 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 0.27 (6169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41562 AN: 151824 Hom.: 6148 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.274 AC: 41618 AN: 151942 Hom.: 6169 Cov.: 31 AF XY: 0.280 AC XY: 20761 AN XY: 74252

African (AFR) AF: 0.229 AC: 9472 AN: 41450

American (AMR) AF: 0.315 AC: 4807 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3129 AN: 5128

South Asian (SAS) AF: 0.431 AC: 2075 AN: 4814

European-Finnish (FIN) AF: 0.262 AC: 2773 AN: 10570

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17139 AN: 67936

Other (OTH) AF: 0.297 AC: 627 AN: 2110

Alfa AF: 0.267 Hom.: 18129

Bravo AF: 0.277

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.64
DANN	Benign	0.58
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs7645716; hg19: chr3-46336781;