6-129712721-G-A

Variant names:

• chr6-129712721-G-A
• rs9385512

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 0.769 in 152,110 control chromosomes in the GnomAD database, including 45,328 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 0.77 (45328 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116854 AN: 151992 Hom.: 45297 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.769 AC: 116940 AN: 152110 Hom.: 45328 Cov.: 31 AF XY: 0.774 AC XY: 57564 AN XY: 74358

African (AFR) AF: 0.700 AC: 29018 AN: 41464

American (AMR) AF: 0.822 AC: 12552 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2694 AN: 3470

East Asian (EAS) AF: 0.938 AC: 4860 AN: 5180

South Asian (SAS) AF: 0.747 AC: 3594 AN: 4810

European-Finnish (FIN) AF: 0.860 AC: 9114 AN: 10594

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52501 AN: 67996

Other (OTH) AF: 0.775 AC: 1636 AN: 2112

Alfa AF: 0.771 Hom.: 74707

Bravo AF: 0.765

Asia WGS AF: 0.827 AC: 2873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.30
DANN	Benign	0.19
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs9385512; hg19: chr6-130033866; COSMIC: COSV63765978;