chr8-88981259-C-T

Variant names:

• chr8-88981259-C-T
• rs10429371

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 0.72 in 151,770 control chromosomes in the GnomAD database, including 40,579 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 0.72 (40579 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 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: 0.720 AC: 109206 AN: 151652 Hom.: 40555 Cov.: 30

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.720 AC: 109269 AN: 151770 Hom.: 40579 Cov.: 30 AF XY: 0.723 AC XY: 53625 AN XY: 74152

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.735

Alfa AF: 0.770 Hom.: 36163

Bravo AF: 0.699

Asia WGS AF: 0.766 AC: 2656 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10429371; hg19: chr8-89993488;