8-2509099-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522799.1(ENSG00000253444):​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: ENSG00000253444 ENST00000522799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

Genes affected

ENSG00000253444 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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
ENSG00000253444	ENST00000522799.1	n.296+1826A>C		intron_variant	Intron 2 of 2	4

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

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.149

Alfa AF: 0.0767 Hom.: 99

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503176; hg19: chr8-2366212;