rs279959

Variant names:

• chr8-93033506-T-C
• rs279959

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;