Genetic Variant ENSG00000302652:n.239+5358G>C (chrX-101690351-G-C) – 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 ENST00000788550.1(ENSG00000302652):n.239+5358G>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 0.78 ( 24039 hom., 25442 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

ENSG00000302652
ENST00000788550.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.117

Publications

0 publications found

Variant links:

Genes affected

ENSG00000302652 (HGNC:):

ENSG00000302652 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=-0.9).

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
ENSG00000302652	ENST00000788550.1 link	n.239+5358G>C		intron_variant	Intron 2 of 2
ENSG00000302652	ENST00000788551.1 link	n.449+5358G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.780

AC:

86257

AN:

110525

Hom.:

24041

Cov.:

show subpopulations

Gnomad AFR

AF:

0.868

Gnomad AMI

AF:

0.937

Gnomad AMR

AF:

0.844

Gnomad ASJ

AF:

0.734

Gnomad EAS

AF:

0.837

Gnomad SAS

AF:

0.840

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.739

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.770

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:

0.780

AC:

86306

AN:

110580

Hom.:

24039

Cov.:

AF XY:

0.776

AC XY:

25442

AN XY:

32792

show subpopulations

African (AFR)

AF:

0.868

AC:

26409

AN:

30434

American (AMR)

AF:

0.844

AC:

8802

AN:

10425

Ashkenazi Jewish (ASJ)

AF:

0.734

AC:

1929

AN:

2628

East Asian (EAS)

AF:

0.838

AC:

2928

AN:

3496

South Asian (SAS)

AF:

0.840

AC:

2180

AN:

2596

European-Finnish (FIN)

AF:

0.613

AC:

3584

AN:

5846

Middle Eastern (MID)

AF:

0.748

AC:

160

AN:

214

European-Non Finnish (NFE)

AF:

0.730

AC:

38531

AN:

52774

Other (OTH)

AF:

0.771

AC:

1145

AN:

1486

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

646

1292

1937

2583

3229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.611

Hom.:

2537

Bravo

AF:

0.801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.45

(source)

PhyloP100

-0.12

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