8-26697814-C-T

Variant names:

• chr8-26697814-C-T
• rs10503789
• ENST00000792407.1:n.85+26940C>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+26940C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,986 control chromosomes in the GnomAD database, including 3,134 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 (3134 hom., cov: 31)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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+26940C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29920 AN: 151868 Hom.: 3136 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.197 AC: 29940 AN: 151986 Hom.: 3134 Cov.: 31 AF XY: 0.194 AC XY: 14382 AN XY: 74274

African (AFR) AF: 0.260 AC: 10762 AN: 41444

American (AMR) AF: 0.140 AC: 2144 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 494 AN: 3464

East Asian (EAS) AF: 0.250 AC: 1285 AN: 5146

South Asian (SAS) AF: 0.112 AC: 539 AN: 4820

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10560

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12228 AN: 67956

Other (OTH) AF: 0.157 AC: 332 AN: 2116

Alfa AF: 0.162 Hom.: 771

Bravo AF: 0.196

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.33
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10503789; hg19: chr8-26555331;