rs2928679

Positions:

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

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 0.628 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.598

Alfa AF: 0.560 Hom.: 48677

Bravo AF: 0.635

Asia WGS AF: 0.707 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2928679; hg19: chr8-23438975;