Genetic Variant ENSG00000228509:n.194+23525A>G (chr2-190792203-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000676095.2(ENSG00000228509):n.194+23525A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,022 control chromosomes in the GnomAD database, including 5,081 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 0.25 ( 5081 hom., cov: 31)

Consequence

ENSG00000228509
ENST00000676095.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.899

Publications

5 publications found

Variant links:

Genes affected

ENSG00000228509 (HGNC:):

ENSG00000228509 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=-0.7).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000228509	ENST00000676095.2 link	n.194+23525A>G	intron_variant	Intron 2 of 8
ENSG00000228509	ENST00000772360.1 link	n.285+23525A>G	intron_variant	Intron 2 of 3
ENSG00000228509	ENST00000772361.1 link	n.180+23525A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37954

AN:

151904

Hom.:

5080

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.247

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

GnomAD4 genome

AF:

0.250

AC:

37974

AN:

152022

Hom.:

5081

Cov.:

AF XY:

0.254

AC XY:

18845

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.182

AC:

7549

AN:

41494

American (AMR)

AF:

0.225

AC:

3438

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

783

AN:

3472

East Asian (EAS)

AF:

0.101

AC:

524

AN:

5188

South Asian (SAS)

AF:

0.322

AC:

1552

AN:

4814

European-Finnish (FIN)

AF:

0.391

AC:

4125

AN:

10556

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19288

AN:

67918

Other (OTH)

AF:

0.246

AC:

519

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1435

2870

4306

5741

7176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.260

Hom.:

881

Bravo

AF:

0.230

Asia WGS

AF:

0.255

AC:

886

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

8.7

(source)

DANN

Benign

0.86

PhyloP100

0.90

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