rs2373154

Variant names:

• chr3-46129606-G-A
• rs2373154

Your query was ambiguous. Multiple possible variants found:

• chr3-46129606-G-A
• chr3-46129606-G-C
• chr3-46129606-G-T

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 0.401 in 151,874 control chromosomes in the GnomAD database, including 13,040 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 0.40 (13040 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 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: 0.401 AC: 60863 AN: 151756 Hom.: 13015 Cov.: 30

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.401 AC: 60935 AN: 151874 Hom.: 13040 Cov.: 30 AF XY: 0.404 AC XY: 30007 AN XY: 74210

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.401

Alfa AF: 0.421 Hom.: 7216

Bravo AF: 0.396

Asia WGS AF: 0.524 AC: 1820 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	0.97
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2373154; hg19: chr3-46171098;