Genetic Variant ENST00000650201.1:n.114-37614C>T (chr18-60441957-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 ENST00000650201.1(ENSG00000285681):n.114-37614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,110 control chromosomes in the GnomAD database, including 39,737 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 0.71 ( 39737 hom., cov: 32)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.279

Publications

5 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=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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.114-37614C>T		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1 link	n.157-37614C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.709

AC:

107771

AN:

151992

Hom.:

39691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.896

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.672

Gnomad ASJ

AF:

0.568

Gnomad EAS

AF:

0.953

Gnomad SAS

AF:

0.682

Gnomad FIN

AF:

0.594

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.615

Gnomad OTH

AF:

0.684

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

GnomAD4 genome

AF:

0.709

AC:

107875

AN:

152110

Hom.:

39737

Cov.:

AF XY:

0.710

AC XY:

52799

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.896

AC:

37243

AN:

41546

American (AMR)

AF:

0.672

AC:

10261

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.568

AC:

1966

AN:

3460

East Asian (EAS)

AF:

0.953

AC:

4936

AN:

5180

South Asian (SAS)

AF:

0.682

AC:

3288

AN:

4824

European-Finnish (FIN)

AF:

0.594

AC:

6261

AN:

10548

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.615

AC:

41812

AN:

67974

Other (OTH)

AF:

0.684

AC:

1446

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1482

2964

4445

5927

7409

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.648

Hom.:

94212

Bravo

AF:

0.725

Asia WGS

AF:

0.848

AC:

2949

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

2.5

(source)

DANN

Benign

0.87

PhyloP100

0.28

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