Genetic Variant ENST00000650201.1:n.113+53078T>C (chr18-60382423-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 ENST00000650201.1(ENSG00000285681):n.113+53078T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 134,694 control chromosomes in the GnomAD database, including 5,898 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 0.23 ( 5898 hom., cov: 31)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140

Publications

17 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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+53078T>C		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1 link	n.156+53078T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

31569

AN:

134574

Hom.:

5865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.0805

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0989

Gnomad OTH

AF:

0.219

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

GnomAD4 genome

AF:

0.235

AC:

31646

AN:

134694

Hom.:

5898

Cov.:

AF XY:

0.234

AC XY:

15104

AN XY:

64612

show subpopulations

African (AFR)

AF:

0.530

AC:

20723

AN:

39122

American (AMR)

AF:

0.195

AC:

2359

AN:

12068

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

324

AN:

3160

East Asian (EAS)

AF:

0.105

AC:

461

AN:

4392

South Asian (SAS)

AF:

0.153

AC:

558

AN:

3638

European-Finnish (FIN)

AF:

0.0805

AC:

632

AN:

7848

Middle Eastern (MID)

AF:

0.103

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.0989

AC:

6093

AN:

61630

Other (OTH)

AF:

0.219

AC:

380

AN:

1738

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1019

2038

3058

4077

5096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.139

Hom.:

565

Bravo

AF:

0.234

Asia WGS

AF:

0.135

AC:

469

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

2.5

(source)

DANN

Benign

0.50

PhyloP100

0.014

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