rs10503790

Variant names:

• chr8-26697926-G-A
• rs10503790
• ENST00000792407.1:n.85+27052G>A

Variant summary

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

The ENST00000792407.1(ENSG00000303169):​n.85+27052G>A 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 152,104 control chromosomes in the GnomAD database, including 3,212 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 (3212 hom., cov: 32)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 4 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=-0.9).
• 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+27052G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30218 AN: 151986 Hom.: 3214 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.186

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: 30238 AN: 152104 Hom.: 3212 Cov.: 32 AF XY: 0.196 AC XY: 14541 AN XY: 74356

African (AFR) AF: 0.266 AC: 11028 AN: 41486

American (AMR) AF: 0.141 AC: 2160 AN: 15294

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

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5164

South Asian (SAS) AF: 0.112 AC: 538 AN: 4818

European-Finnish (FIN) AF: 0.186 AC: 1965 AN: 10574

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

European-Non Finnish (NFE) AF: 0.180 AC: 12236 AN: 67982

Other (OTH) AF: 0.158 AC: 334 AN: 2110

Alfa AF: 0.195 Hom.: 544

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	-0.90
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10503790; hg19: chr8-26555443;