6-30927667-A-G

Variant names:

• chr6-30927667-A-G
• rs2532932

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 0.746 in 152,072 control chromosomes in the GnomAD database, including 42,793 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 0.75 (42793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113377 AN: 151954 Hom.: 42748 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.746 AC: 113473 AN: 152072 Hom.: 42793 Cov.: 32 AF XY: 0.751 AC XY: 55800 AN XY: 74324

African (AFR) AF: 0.635 AC: 26326 AN: 41430

American (AMR) AF: 0.774 AC: 11839 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3077 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4867 AN: 5176

South Asian (SAS) AF: 0.902 AC: 4357 AN: 4828

European-Finnish (FIN) AF: 0.793 AC: 8380 AN: 10572

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52103 AN: 67988

Other (OTH) AF: 0.728 AC: 1538 AN: 2114

Alfa AF: 0.772 Hom.: 31641

Bravo AF: 0.739

Asia WGS AF: 0.889 AC: 3093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.57
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2532932; hg19: chr6-30895444;