Genetic Variant ENSG00000297719:n.234-30190C>T (chrX-134983524-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000750476.1(ENSG00000297719):n.234-30190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 111,089 control chromosomes in the GnomAD database, including 5,722 homozygotes. There are 11,793 hemizygotes in GnomAD. 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 0.37 ( 5722 hom., 11793 hem., cov: 23)

Consequence

ENSG00000297719
ENST00000750476.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Publications

0 publications found

Variant links:

Genes affected

ENSG00000297719 (HGNC:):

ENSG00000297719 links:

Genome browser will be placed here

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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
ENSG00000297719	ENST00000750476.1 link	n.234-30190C>T		intron_variant	Intron 1 of 1
ENSG00000297719	ENST00000750477.1 link	n.753-30190C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

40678

AN:

111034

Hom.:

5720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.504

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.450

Gnomad FIN

AF:

0.237

Gnomad MID

AF:

0.477

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.380

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

GnomAD4 genome

AF:

0.366

AC:

40694

AN:

111089

Hom.:

5722

Cov.:

AF XY:

0.354

AC XY:

11793

AN XY:

33325

show subpopulations

African (AFR)

AF:

0.504

AC:

15373

AN:

30513

American (AMR)

AF:

0.276

AC:

2899

AN:

10516

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

926

AN:

2630

East Asian (EAS)

AF:

0.457

AC:

1591

AN:

3483

South Asian (SAS)

AF:

0.451

AC:

1185

AN:

2630

European-Finnish (FIN)

AF:

0.237

AC:

1419

AN:

5978

Middle Eastern (MID)

AF:

0.474

AC:

102

AN:

215

European-Non Finnish (NFE)

AF:

0.311

AC:

16455

AN:

52935

Other (OTH)

AF:

0.377

AC:

571

AN:

1516

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

902

1804

2706

3608

4510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.338

Hom.:

38839

Bravo

AF:

0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.4

(source)

DANN

Benign

0.47

PhyloP100

-0.040

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