rs1587126

Variant names:

• chr3-30327603-C-A
• rs1587126

Your query was ambiguous. Multiple possible variants found:

• chr3-30327603-C-A
• chr3-30327603-C-G
• chr3-30327603-C-T

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 0.731 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.812 AC: 33409 AN: 41126

American (AMR) AF: 0.746 AC: 11227 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2219 AN: 3456

East Asian (EAS) AF: 0.825 AC: 4197 AN: 5090

South Asian (SAS) AF: 0.820 AC: 3930 AN: 4790

European-Finnish (FIN) AF: 0.699 AC: 7093 AN: 10150

Middle Eastern (MID) AF: 0.610 AC: 177 AN: 290

European-Non Finnish (NFE) AF: 0.675 AC: 45476 AN: 67352

Other (OTH) AF: 0.693 AC: 1447 AN: 2088

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
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs1587126; hg19: chr3-30369095;