Genetic Variant ENSG00000282142:n.296+2390C>A (chr8-2508535-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

Publications

3 publications found

Variant links:

Genes affected

ENSG00000282142 (HGNC:):

ENSG00000282142 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000282142	ENST00000522799.1 link	n.296+2390C>A	intron_variant	Intron 2 of 2	4
ENSG00000282142	ENST00000825372.1 link	n.483+2390C>A	intron_variant	Intron 3 of 3
ENSG00000282142	ENST00000825373.1 link	n.480+2390C>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56404

AN:

151876

Hom.:

14129

Cov.:

show subpopulations

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.:

AF XY:

0.361

AC XY:

26816

AN XY:

74282

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1471

2941

4412

5882

7353

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.13

(source)

DANN

Benign

0.28

PhyloP100

-1.3

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over