8-2509099-T-G

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, non coding transcript 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: ENST00000522799.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522799.1	n.296+1826A>C		intron_variant, non_coding_transcript_variant		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;