rs10503788

Variant names:

• chr8-26697629-C-T
• rs10503788
• ENST00000792407.1:n.85+26755C>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+26755C>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 152,030 control chromosomes in the GnomAD database, including 3,124 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 (3124 hom., cov: 31)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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+26755C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29917 AN: 151912 Hom.: 3126 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: 0.185

Gnomad MID AF: 0.161

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: 29937 AN: 152030 Hom.: 3124 Cov.: 31 AF XY: 0.194 AC XY: 14375 AN XY: 74284

African (AFR) AF: 0.259 AC: 10748 AN: 41452

American (AMR) AF: 0.140 AC: 2143 AN: 15266

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

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5172

South Asian (SAS) AF: 0.112 AC: 538 AN: 4808

European-Finnish (FIN) AF: 0.185 AC: 1958 AN: 10556

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

European-Non Finnish (NFE) AF: 0.180 AC: 12238 AN: 67984

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.177 Hom.: 1520

Bravo AF: 0.196

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.78
DANN	Benign	0.35
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs10503788; hg19: chr8-26555146;