rs10429371

Variant names:

• chr8-88981259-C-T
• rs10429371

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.529 AC: 21851 AN: 41338

American (AMR) AF: 0.725 AC: 11008 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2993 AN: 3464

East Asian (EAS) AF: 0.739 AC: 3802 AN: 5146

South Asian (SAS) AF: 0.795 AC: 3833 AN: 4822

European-Finnish (FIN) AF: 0.852 AC: 9033 AN: 10598

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.798 AC: 54187 AN: 67910

Other (OTH) AF: 0.735 AC: 1553 AN: 2112

Alfa AF: 0.764 Hom.: 100653

Bravo AF: 0.699

Asia WGS AF: 0.766 AC: 2656 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.57
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs10429371; hg19: chr8-89993488;