Genetic Variant ENSG00000286797:n.540+27031C>G (chr2-185461222-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000655441.1(ENSG00000286797):n.540+27031C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,880 control chromosomes in the GnomAD database, including 4,470 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 0.22 ( 4470 hom., cov: 32)

Consequence

ENSG00000286797
ENST00000655441.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.348

Publications

3 publications found

Variant links:

Genes affected

ENSG00000286797 (HGNC:):

ENSG00000286797 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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286797	ENST00000655441.1 link	n.540+27031C>G	intron_variant	Intron 2 of 2
ENSG00000286797	ENST00000671641.1 link	n.311-21812C>G	intron_variant	Intron 2 of 3
ENSG00000286797	ENST00000799165.1 link	n.253-21812C>G	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

33966

AN:

151762

Hom.:

4462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.397

Gnomad FIN

AF:

0.388

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.196

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

GnomAD4 genome

AF:

0.224

AC:

33969

AN:

151880

Hom.:

4470

Cov.:

AF XY:

0.232

AC XY:

17230

AN XY:

74190

show subpopulations

African (AFR)

AF:

0.133

AC:

5528

AN:

41448

American (AMR)

AF:

0.148

AC:

2259

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

494

AN:

3466

East Asian (EAS)

AF:

0.391

AC:

2024

AN:

5170

South Asian (SAS)

AF:

0.398

AC:

1919

AN:

4824

European-Finnish (FIN)

AF:

0.388

AC:

4086

AN:

10524

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.251

AC:

17052

AN:

67908

Other (OTH)

AF:

0.202

AC:

426

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1278

2555

3833

5110

6388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.243

Hom.:

657

Bravo

AF:

0.196

Asia WGS

AF:

0.376

AC:

1302

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.80

(source)

DANN

Benign

0.42

PhyloP100

-0.35

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