6-32702531-A-G

Variant names:

• chr6-32702531-A-G
• rs2856717

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 0.646 in 151,944 control chromosomes in the GnomAD database, including 32,083 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 0.65 (32083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98010 AN: 151826 Hom.: 32061 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.646 AC: 98084 AN: 151944 Hom.: 32083 Cov.: 31 AF XY: 0.650 AC XY: 48279 AN XY: 74276

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.689

Alfa AF: 0.631 Hom.: 43482

Bravo AF: 0.656

Asia WGS AF: 0.769 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2856717; hg19: chr6-32670308;