rs2858324

Positions:

• chr6-32692598-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;