rs2928679

Variant names:

• chr8-23581462-A-G
• rs2928679

Your query was ambiguous. Multiple possible variants found:

• chr8-23581462-A-G
• chr8-23581462-A-T

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 0.628 in 152,022 control chromosomes in the GnomAD database, including 31,000 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 0.63 (31000 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 64 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95415 AN: 151904 Hom.: 30959 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.628 AC: 95519 AN: 152022 Hom.: 31000 Cov.: 31 AF XY: 0.636 AC XY: 47266 AN XY: 74328

African (AFR) AF: 0.736 AC: 30526 AN: 41470

American (AMR) AF: 0.662 AC: 10112 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4419 AN: 5156

South Asian (SAS) AF: 0.531 AC: 2557 AN: 4812

European-Finnish (FIN) AF: 0.675 AC: 7133 AN: 10564

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37094 AN: 67962

Other (OTH) AF: 0.598 AC: 1260 AN: 2106

Alfa AF: 0.574 Hom.: 75995

Bravo AF: 0.635

Asia WGS AF: 0.707 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.048
DANN	Benign	0.59
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2928679; hg19: chr8-23438975;