3-157059338-T-C

Variant names:

• chr3-157059338-T-C
• rs2046273

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 0.622 in 152,062 control chromosomes in the GnomAD database, including 31,712 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 0.62 (31712 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.622 AC: 94537 AN: 151944 Hom.: 31698 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.622 AC: 94578 AN: 152062 Hom.: 31712 Cov.: 32 AF XY: 0.632 AC XY: 47019 AN XY: 74342

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.630

Alfa AF: 0.690 Hom.: 14900

Bravo AF: 0.607

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046273; hg19: chr3-156777127;