chr3-46295290-G-A

Position:

• chr3-46295290-G-A

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 0.274 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.297

Alfa AF: 0.269 Hom.: 11767

Bravo AF: 0.277

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7645716; hg19: chr3-46336781;