Genetic Variant ENST00000653446.1:n.287-98281G>T (chrX-33978185-G-T) – 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 ENST00000653446.1(ENSG00000233928):n.287-98281G>T 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 0.79 ( 24572 hom., 25065 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000233928
ENST00000653446.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.330

Publications

1 publications found

Variant links:

Genes affected

ENSG00000233928 (HGNC:):

ENSG00000233928 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=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000233928	ENST00000653446.1	n.287-98281G>T	intron	N/A
ENSG00000233928	ENST00000656777.1	n.349-98281G>T	intron	N/A
ENSG00000233928	ENST00000656973.1	n.201-98281G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.792

AC:

86646

AN:

109438

Hom.:

24578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.801

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.866

Gnomad EAS

AF:

0.563

Gnomad SAS

AF:

0.707

Gnomad FIN

AF:

0.796

Gnomad MID

AF:

0.859

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.811

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:

0.792

AC:

86674

AN:

109486

Hom.:

24572

Cov.:

AF XY:

0.788

AC XY:

25065

AN XY:

31800

show subpopulations

African (AFR)

AF:

0.825

AC:

24751

AN:

30013

American (AMR)

AF:

0.821

AC:

8423

AN:

10257

Ashkenazi Jewish (ASJ)

AF:

0.866

AC:

2275

AN:

2627

East Asian (EAS)

AF:

0.562

AC:

1925

AN:

3424

South Asian (SAS)

AF:

0.707

AC:

1787

AN:

2527

European-Finnish (FIN)

AF:

0.796

AC:

4559

AN:

5724

Middle Eastern (MID)

AF:

0.859

AC:

183

AN:

213

European-Non Finnish (NFE)

AF:

0.781

AC:

41020

AN:

52524

Other (OTH)

AF:

0.806

AC:

1207

AN:

1498

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

665

1330

1995

2660

3325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<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:

0.787

Hom.:

8583

Bravo

AF:

0.800

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.8

(source)

DANN

Benign

0.38

PhyloP100

0.33

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over