Genetic Variant ENSG00000303258:n.142-20224G>T (chr2-85478554-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000793246.1(ENSG00000303258):n.142-20224G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0381 in 152,272 control chromosomes in the GnomAD database, including 143 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 0.038 ( 143 hom., cov: 32)

Consequence

ENSG00000303258
ENST00000793246.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

10 publications found

Variant links:

Genes affected

ENSG00000303258 (HGNC:):

ENSG00000303258 links:

Genome browser will be placed here

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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000303258	ENST00000793246.1 link	n.142-20224G>T	intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793247.1 link	n.347-20224G>T	intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793248.1 link	n.340-20198G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0380

AC:

5788

AN:

152154

Hom.:

141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0113

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.0380

Gnomad ASJ

AF:

0.0397

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0478

Gnomad FIN

AF:

0.0478

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0545

Gnomad OTH

AF:

0.0340

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

GnomAD4 genome

AF:

0.0381

AC:

5795

AN:

152272

Hom.:

143

Cov.:

AF XY:

0.0372

AC XY:

2773

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0113

AC:

470

AN:

41562

American (AMR)

AF:

0.0385

AC:

588

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0397

AC:

138

AN:

3472

East Asian (EAS)

AF:

0.000964

AC:

AN:

5186

South Asian (SAS)

AF:

0.0483

AC:

233

AN:

4826

European-Finnish (FIN)

AF:

0.0478

AC:

507

AN:

10608

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0545

AC:

3709

AN:

68010

Other (OTH)

AF:

0.0336

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

288

577

865

1154

1442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0388

Hom.:

152

Bravo

AF:

0.0360

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.8

(source)

DANN

Benign

0.71

PhyloP100

0.21

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