rs279959

Variant names:

• chr8-93033506-T-C
• rs279959

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.413 AC: 17113 AN: 41456

American (AMR) AF: 0.802 AC: 12270 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2589 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2710 AN: 5172

South Asian (SAS) AF: 0.712 AC: 3435 AN: 4826

European-Finnish (FIN) AF: 0.816 AC: 8630 AN: 10582

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55500 AN: 67988

Other (OTH) AF: 0.706 AC: 1490 AN: 2110

Alfa AF: 0.706 Hom.: 4021

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs279959; hg19: chr8-94045734;