rs279959

chr8-93033506-T-C

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 0.688 in 152,104 control chromosomes in the GnomAD database, including 38,405 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 0.69 (38405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 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: 0.688 AC: 104577 AN: 151986 Hom.: 38394 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.688 AC: 104614 AN: 152104 Hom.: 38405 Cov.: 32 AF XY: 0.691 AC XY: 51404 AN XY: 74360

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.706

Alfa AF: 0.721 Hom.: 3947

Bravo AF: 0.673

Asia WGS AF: 0.577 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.59
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs279959; hg19: chr8-94045734;