rs10503429

Variant names:

• chr8-12824206-A-G
• rs10503429

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 0.167 in 152,220 control chromosomes in the GnomAD database, including 2,258 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 0.17 (2258 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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 (NFE) allele frequency at 95% confidence interval = 0.208 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: 0.167 AC: 25471 AN: 152102 Hom.: 2254 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.167 AC: 25491 AN: 152220 Hom.: 2258 Cov.: 33 AF XY: 0.163 AC XY: 12163 AN XY: 74422

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.162

Alfa AF: 0.195 Hom.: 3959

Bravo AF: 0.161

Asia WGS AF: 0.189 AC: 657 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	5.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503429; hg19: chr8-12681715;