rs10503429

Variant names:

• chr8-12824206-A-G
• rs10503429
• ENST00000838107.1:n.*236T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000838107.1(ENSG00000309058):​n.*236T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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: ENSG00000309058 ENST00000838107.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 4 publications found

Genes affected

ENSG00000309058 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000309058	ENST00000838107.1	n.*236T>C		downstream_gene_variant

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

African (AFR) AF: 0.115 AC: 4772 AN: 41556

American (AMR) AF: 0.112 AC: 1717 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3470

East Asian (EAS) AF: 0.169 AC: 875 AN: 5186

South Asian (SAS) AF: 0.195 AC: 940 AN: 4826

European-Finnish (FIN) AF: 0.160 AC: 1694 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14354 AN: 67982

Other (OTH) AF: 0.162 AC: 342 AN: 2110

Alfa AF: 0.191 Hom.: 4866

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10503429; hg19: chr8-12681715;