8-2508535-G-T

Position:

• chr8-2508535-G-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(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/exons	MANE	Protein	UniProt
		n.2508535G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253444	ENST00000522799.1	n.296+2390C>A		intron_variant		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;