rs325129

chr6-147486007-G-Achr6-147486007-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;