8-2508535-G-T

Variant names:

• chr8-2508535-G-T
• rs2100623
• ENST00000522799.1:n.296+2390C>A

Variant summary

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

The ENST00000522799.1(ENSG00000253444):​n.296+2390C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,994 control chromosomes in the GnomAD database, including 14,152 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 0.37 (14152 hom., cov: 33)
• Consequence: ENSG00000253444 ENST00000522799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

ENSG00000253444 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 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+2390C>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56404 AN: 151876 Hom.: 14129 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.372 AC: 56472 AN: 151994 Hom.: 14152 Cov.: 33 AF XY: 0.361 AC XY: 26816 AN XY: 74282

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.357

Alfa AF: 0.245 Hom.: 3647

Bravo AF: 0.394

Asia WGS AF: 0.215 AC: 750 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2100623; hg19: chr8-2365648;