ENST00000522799.1:n.296+1826A>C

Variant names:

• chr8-2509099-T-G
• rs10503176
• ENST00000522799.1:n.296+1826A>C

Variant summary

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

The ENST00000522799.1(ENSG00000282142):​n.296+1826A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,186 control chromosomes in the GnomAD database, including 1,941 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 0.15 (1941 hom., cov: 33)
• Consequence: ENSG00000282142 ENST00000522799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877
• Publications: 0 publications found

Genes affected

ENSG00000282142 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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
ENSG00000282142	ENST00000522799.1	n.296+1826A>C		intron_variant	Intron 2 of 2	4
ENSG00000282142	ENST00000825372.1	n.483+1826A>C		intron_variant	Intron 3 of 3
ENSG00000282142	ENST00000825373.1	n.480+1826A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23299 AN: 152070 Hom.: 1942 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23322 AN: 152186 Hom.: 1941 Cov.: 33 AF XY: 0.153 AC XY: 11373 AN XY: 74408

African (AFR) AF: 0.222 AC: 9227 AN: 41504

American (AMR) AF: 0.142 AC: 2173 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1075 AN: 5182

South Asian (SAS) AF: 0.101 AC: 485 AN: 4822

European-Finnish (FIN) AF: 0.122 AC: 1292 AN: 10604

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8173 AN: 67990

Other (OTH) AF: 0.149 AC: 316 AN: 2114

Alfa AF: 0.116 Hom.: 386

Bravo AF: 0.161

Asia WGS AF: 0.162 AC: 564 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs10503176; hg19: chr8-2366212;