8-2508535-G-T

Variant names:

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

Variant summary

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

The ENST00000522799.1(ENSG00000282142):​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: ENSG00000282142 ENST00000522799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522799.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282142	ENST00000522799.1	TSL:4	n.296+2390C>A		intron	N/A
	ENSG00000282142	ENST00000825372.1		n.483+2390C>A		intron	N/A
	ENSG00000282142	ENST00000825373.1		n.480+2390C>A		intron	N/A

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

African (AFR) AF: 0.724 AC: 30022 AN: 41452

American (AMR) AF: 0.261 AC: 3982 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1148 AN: 3462

East Asian (EAS) AF: 0.192 AC: 998 AN: 5186

South Asian (SAS) AF: 0.165 AC: 794 AN: 4822

European-Finnish (FIN) AF: 0.185 AC: 1952 AN: 10526

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16492 AN: 67954

Other (OTH) AF: 0.357 AC: 753 AN: 2110

Alfa AF: 0.282 Hom.: 16542

Bravo AF: 0.394

Asia WGS AF: 0.215 AC: 750 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.28
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2100623;

hg19: chr8-2365648;