Genetic Variant ENSG00000287083:n.504-17158G>A (chr4-180038549-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 ENST00000663768.1(ENSG00000287083):n.504-17158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,030 control chromosomes in the GnomAD database, including 7,922 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 0.26 ( 7922 hom., cov: 32)

Consequence

ENSG00000287083
ENST00000663768.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.700

Publications

0 publications found

Variant links:

Genes affected

ENSG00000287083 (HGNC:):

ENSG00000287083 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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287083	ENST00000663768.1 link	n.504-17158G>A	intron_variant	Intron 2 of 6
ENSG00000287083	ENST00000826563.1 link	n.147-17158G>A	intron_variant	Intron 1 of 6
ENSG00000287083	ENST00000826564.1 link	n.256-17158G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39836

AN:

151912

Hom.:

7896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.551

Gnomad AMI

AF:

0.0571

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.263

AC:

39923

AN:

152030

Hom.:

7922

Cov.:

AF XY:

0.265

AC XY:

19703

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.551

AC:

22845

AN:

41438

American (AMR)

AF:

0.267

AC:

4074

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

663

AN:

3472

East Asian (EAS)

AF:

0.252

AC:

1297

AN:

5140

South Asian (SAS)

AF:

0.273

AC:

1314

AN:

4820

European-Finnish (FIN)

AF:

0.101

AC:

1071

AN:

10598

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.118

AC:

8023

AN:

67978

Other (OTH)

AF:

0.243

AC:

513

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1262

2525

3787

5050

6312

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:

0.0807

Hom.:

142

Bravo

AF:

0.287

Asia WGS

AF:

0.311

AC:

1080

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.87

(source)

DANN

Benign

0.13

PhyloP100

-0.70

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