6-32713500-A-G

Variant names:

• chr6-32713500-A-G
• rs2858331

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 0.427 in 151,956 control chromosomes in the GnomAD database, including 14,205 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 0.43 (14205 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 67 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64766 AN: 151836 Hom.: 14197 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.427 AC: 64810 AN: 151956 Hom.: 14205 Cov.: 31 AF XY: 0.424 AC XY: 31543 AN XY: 74312

African (AFR) AF: 0.474 AC: 19628 AN: 41434

American (AMR) AF: 0.438 AC: 6681 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1829 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2245 AN: 5166

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4818

European-Finnish (FIN) AF: 0.328 AC: 3468 AN: 10562

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26637 AN: 67926

Other (OTH) AF: 0.500 AC: 1056 AN: 2110

Alfa AF: 0.398 Hom.: 48902

Bravo AF: 0.435

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.47
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2858331; hg19: chr6-32681277;