6-32692598-A-G

Variant names:

• chr6-32692598-A-G
• rs2858324

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 0.639 in 151,530 control chromosomes in the GnomAD database, including 31,332 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 0.64 (31332 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 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: 0.639 AC: 96762 AN: 151412 Hom.: 31310 Cov.: 30

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.639 AC: 96835 AN: 151530 Hom.: 31332 Cov.: 30 AF XY: 0.643 AC XY: 47615 AN XY: 74004

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.681

Alfa AF: 0.621 Hom.: 14195

Bravo AF: 0.650

Asia WGS AF: 0.766 AC: 2661 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.83
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858324; hg19: chr6-32660375;