chr8-24926467-C-T

Position:

• chr8-24926467-C-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 0.89 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/exons	MANE	UniProt

Ensembl

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