rs325129

Variant names:

• chr6-147486007-G-A
• rs325129

Your query was ambiguous. Multiple possible variants found:

• chr6-147486007-G-A
• chr6-147486007-G-C

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 151,958 control chromosomes in the GnomAD database, including 29,686 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 (29686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 91527 AN: 151838 Hom.: 29670 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.670

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.603 AC: 91598 AN: 151958 Hom.: 29686 Cov.: 32 AF XY: 0.601 AC XY: 44636 AN XY: 74288

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.636

Alfa AF: 0.688 Hom.: 15043

Bravo AF: 0.585

Asia WGS AF: 0.497 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs325129; hg19: chr6-147807143;