8-124281001-T-C

Variant names:

• chr8-124281001-T-C
• rs10808533

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 0.66 in 152,100 control chromosomes in the GnomAD database, including 33,161 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 0.66 (33161 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.660 AC: 100289 AN: 151982 Hom.: 33116 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.660 AC: 100382 AN: 152100 Hom.: 33161 Cov.: 33 AF XY: 0.659 AC XY: 49005 AN XY: 74364

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.670

Alfa AF: 0.660 Hom.: 57648

Bravo AF: 0.671

Asia WGS AF: 0.695 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10808533; hg19: chr8-125293242;