rs10503794

Variant names:

• chr8-26699248-C-T
• rs10503794
• ENST00000792407.1:n.85+28374C>T

Variant summary

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

The ENST00000792407.1(ENSG00000303169):​n.85+28374C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,130 control chromosomes in the GnomAD database, including 3,214 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 0.20 (3214 hom., cov: 32)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 1 publications found

Genes affected

ENSG00000303169 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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
ENSG00000303169	ENST00000792407.1	n.85+28374C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30240 AN: 152012 Hom.: 3216 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.199 AC: 30260 AN: 152130 Hom.: 3214 Cov.: 32 AF XY: 0.196 AC XY: 14562 AN XY: 74376

African (AFR) AF: 0.266 AC: 11033 AN: 41488

American (AMR) AF: 0.141 AC: 2156 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1294 AN: 5176

South Asian (SAS) AF: 0.113 AC: 542 AN: 4814

European-Finnish (FIN) AF: 0.187 AC: 1976 AN: 10584

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12239 AN: 67988

Other (OTH) AF: 0.158 AC: 333 AN: 2108

Alfa AF: 0.202 Hom.: 426

Bravo AF: 0.199

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.090
DANN	Benign	0.77
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10503794; hg19: chr8-26556765;