Genetic Variant ENSG00000286272:n.195+1546G>A (chr2-221034724-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000830589.1(ENSG00000286272):n.195+1546G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,140 control chromosomes in the GnomAD database, including 2,563 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 0.17 ( 2563 hom., cov: 32)

Consequence

ENSG00000286272
ENST00000830589.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.166

Publications

12 publications found

Variant links:

Genes affected

ENSG00000286272 (HGNC:):

ENSG00000286272 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 (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286272	ENST00000830589.1 link	n.195+1546G>A	intron_variant	Intron 2 of 4
ENSG00000286272	ENST00000830590.1 link	n.198+1546G>A	intron_variant	Intron 2 of 3
ENSG00000286272	ENST00000830591.1 link	n.145+1546G>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26475

AN:

152022

Hom.:

2561

Cov.:

show subpopulations

Gnomad AFR

AF:

0.252

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.166

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

GnomAD4 genome

AF:

0.174

AC:

26508

AN:

152140

Hom.:

2563

Cov.:

AF XY:

0.171

AC XY:

12692

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.252

AC:

10434

AN:

41464

American (AMR)

AF:

0.134

AC:

2047

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

675

AN:

3466

East Asian (EAS)

AF:

0.123

AC:

637

AN:

5180

South Asian (SAS)

AF:

0.146

AC:

704

AN:

4830

European-Finnish (FIN)

AF:

0.107

AC:

1138

AN:

10590

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.152

AC:

10356

AN:

68008

Other (OTH)

AF:

0.167

AC:

353

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1108

2216

3325

4433

5541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.159

Hom.:

7790

Bravo

AF:

0.180

Asia WGS

AF:

0.136

AC:

471

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

6.7

(source)

DANN

Benign

0.65

PhyloP100

0.17

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