Genetic Variant ENST00000653599.1:n.282+69102A>C (chrX-96302380-T-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000653599.1(ENSG00000286523):n.282+69102A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.93 ( 33210 hom., 29716 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000286523
ENST00000653599.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.943

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286523 (HGNC:):

ENSG00000286523 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286523	ENST00000653599.1 link	n.282+69102A>C	intron_variant	Intron 2 of 4
ENSG00000286523	ENST00000669252.1 link	n.750+57186A>C	intron_variant	Intron 5 of 7
ENSG00000286523	ENST00000752891.1 link	n.223+70098A>C	intron_variant	Intron 1 of 5
ENSG00000286523	ENST00000752892.1 link	n.267+69102A>C	intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.925

AC:

101492

AN:

109666

Hom.:

33215

Cov.:

show subpopulations

Gnomad AFR

AF:

0.883

Gnomad AMI

AF:

0.921

Gnomad AMR

AF:

0.951

Gnomad ASJ

AF:

0.976

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.992

Gnomad FIN

AF:

0.945

Gnomad MID

AF:

0.924

Gnomad NFE

AF:

0.933

Gnomad OTH

AF:

0.917

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.925

AC:

101535

AN:

109716

Hom.:

33210

Cov.:

AF XY:

0.929

AC XY:

29716

AN XY:

31980

show subpopulations

African (AFR)

AF:

0.883

AC:

26688

AN:

30231

American (AMR)

AF:

0.951

AC:

9683

AN:

10184

Ashkenazi Jewish (ASJ)

AF:

0.976

AC:

2563

AN:

2625

East Asian (EAS)

AF:

0.999

AC:

3510

AN:

3512

South Asian (SAS)

AF:

0.992

AC:

2519

AN:

2540

European-Finnish (FIN)

AF:

0.945

AC:

5332

AN:

5643

Middle Eastern (MID)

AF:

0.921

AC:

198

AN:

215

European-Non Finnish (NFE)

AF:

0.933

AC:

49050

AN:

52597

Other (OTH)

AF:

0.917

AC:

1374

AN:

1498

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

281

561

842

1122

1403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<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:

0.937

Hom.:

40585

Bravo

AF:

0.925

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.75

(source)

DANN

Benign

0.42

PhyloP100

-0.94

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