6-30929997-A-G

Variant names:

• chr6-30929997-A-G
• rs2532929

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 0.335 in 151,922 control chromosomes in the GnomAD database, including 9,857 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 0.34 (9857 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 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: 0.335 AC: 50929 AN: 151804 Hom.: 9846 Cov.: 30

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.335 AC: 50960 AN: 151922 Hom.: 9857 Cov.: 30 AF XY: 0.343 AC XY: 25484 AN XY: 74236

African (AFR) AF: 0.135 AC: 5582 AN: 41448

American (AMR) AF: 0.456 AC: 6971 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1669 AN: 3464

East Asian (EAS) AF: 0.509 AC: 2620 AN: 5152

South Asian (SAS) AF: 0.445 AC: 2144 AN: 4822

European-Finnish (FIN) AF: 0.438 AC: 4619 AN: 10536

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26196 AN: 67896

Other (OTH) AF: 0.353 AC: 746 AN: 2112

Alfa AF: 0.382 Hom.: 46056

Bravo AF: 0.328

Asia WGS AF: 0.453 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2532929; hg19: chr6-30897774;