rs1587126

chr3-30327603-C-Achr3-30327603-C-Gchr3-30327603-C-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 0.731 in 150,298 control chromosomes in the GnomAD database, including 40,531 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 0.73 (40531 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.731 AC: 109777 AN: 150182 Hom.: 40489 Cov.: 29

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.731 AC: 109880 AN: 150298 Hom.: 40531 Cov.: 29 AF XY: 0.735 AC XY: 53867 AN XY: 73312

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.693

Alfa AF: 0.708 Hom.: 4731

Bravo AF: 0.733

Asia WGS AF: 0.805 AC: 2794 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.79
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1587126; hg19: chr3-30369095;