8-24958616-C-T

Variant names:

• chr8-24958616-C-T
• rs2976437

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 0.547 in 151,950 control chromosomes in the GnomAD database, including 24,457 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 (24457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 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: 0.547 AC: 83094 AN: 151832 Hom.: 24447 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.547 AC: 83133 AN: 151950 Hom.: 24457 Cov.: 31 AF XY: 0.551 AC XY: 40917 AN XY: 74254

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.548

Alfa AF: 0.574 Hom.: 5145

Bravo AF: 0.541

Asia WGS AF: 0.642 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
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: rs2976437; hg19: chr8-24816130;