8-24926467-C-T

Variant names:

• chr8-24926467-C-T
• rs196854

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 0.89 in 152,248 control chromosomes in the GnomAD database, including 60,397 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 0.89 (60397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.890 AC: 135428 AN: 152130 Hom.: 60353 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.890 AC: 135530 AN: 152248 Hom.: 60397 Cov.: 32 AF XY: 0.890 AC XY: 66236 AN XY: 74426

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.894

Alfa AF: 0.876 Hom.: 9191

Bravo AF: 0.900

Asia WGS AF: 0.931 AC: 3235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs196854; hg19: chr8-24783980;