rs325124

Variant names:

• chr6-147484313-C-A
• rs325124

Your query was ambiguous. Multiple possible variants found:

• chr6-147484313-C-A
• chr6-147484313-C-G

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 0.603 in 152,040 control chromosomes in the GnomAD database, including 29,694 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 0.60 (29694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 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: 0.603 AC: 91604 AN: 151922 Hom.: 29676 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.603 AC: 91679 AN: 152040 Hom.: 29694 Cov.: 32 AF XY: 0.601 AC XY: 44677 AN XY: 74330

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.635

Alfa AF: 0.566 Hom.: 1976

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs325124; hg19: chr6-147805449;