rs2979684

Positions:

• chr8-24959927-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;