chr8-24959927-G-A

Variant names:

• chr8-24959927-G-A
• rs2979684

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 0.546 in 151,846 control chromosomes in the GnomAD database, including 24,373 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 0.55 (24373 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 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: 0.546 AC: 82861 AN: 151728 Hom.: 24363 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.546 AC: 82898 AN: 151846 Hom.: 24373 Cov.: 31 AF XY: 0.550 AC XY: 40814 AN XY: 74230

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.547

Alfa AF: 0.603 Hom.: 7112

Bravo AF: 0.540

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2979684; hg19: chr8-24817441;