Genetic Variant ENSG00000285681:n.113+33488T>A (chr18-60362833-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000650201.1(ENSG00000285681):n.113+33488T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,038 control chromosomes in the GnomAD database, including 11,918 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 0.38 ( 11918 hom., cov: 33)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.365

Publications

12 publications found

Variant links:

Genes affected

ENSG00000285681 (HGNC:):

ENSG00000285681 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285681	ENST00000650201.1 link	n.113+33488T>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1 link	n.156+33488T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

58130

AN:

151920

Hom.:

11896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.527

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.383

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.370

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

GnomAD4 genome

AF:

0.383

AC:

58189

AN:

152038

Hom.:

11918

Cov.:

AF XY:

0.374

AC XY:

27832

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.528

AC:

21885

AN:

41486

American (AMR)

AF:

0.383

AC:

5842

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.298

AC:

1034

AN:

3466

East Asian (EAS)

AF:

0.211

AC:

1092

AN:

5176

South Asian (SAS)

AF:

0.347

AC:

1673

AN:

4824

European-Finnish (FIN)

AF:

0.247

AC:

2618

AN:

10582

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.337

AC:

22858

AN:

67920

Other (OTH)

AF:

0.367

AC:

775

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1806

3611

5417

7222

9028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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:

0.357

Hom.:

1452

Bravo

AF:

0.404

Asia WGS

AF:

0.275

AC:

957

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.3

(source)

DANN

Benign

0.43

PhyloP100

-0.36

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