3-30327603-C-A

Variant names:

• chr3-30327603-C-A
• rs1587126

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 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

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;