Genetic Variant ENSG00000228427:n.268-2030A>G (chrX-71186047-T-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 ENST00000450860.1(ENSG00000228427):n.268-2030A>G 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 0.54 ( 12572 hom., 12961 hem., cov: 18)

Failed GnomAD Quality Control

Consequence

ENSG00000228427
ENST00000450860.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03

Publications

2 publications found

Variant links:

Genes affected

ENSG00000228427 (HGNC:):

ENSG00000228427 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
LOC107985688	XR_001755878.2 link	n.286-2030A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000228427	ENST00000450860.1 link	n.268-2030A>G	intron_variant	Intron 1 of 1	3
ENSG00000228427	ENST00000652147.3 link	n.358-2034A>G	intron_variant	Intron 1 of 1
ENSG00000228427	ENST00000664514.4 link	n.600-2030A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

54421

AN:

101218

Hom.:

12566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.800

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.595

Gnomad ASJ

AF:

0.599

Gnomad EAS

AF:

0.711

Gnomad SAS

AF:

0.555

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.590

Gnomad NFE

AF:

0.384

Gnomad OTH

AF:

0.580

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:

0.538

AC:

54459

AN:

101254

Hom.:

12572

Cov.:

AF XY:

0.525

AC XY:

12961

AN XY:

24708

show subpopulations

African (AFR)

AF:

0.800

AC:

22115

AN:

27628

American (AMR)

AF:

0.595

AC:

5461

AN:

9181

Ashkenazi Jewish (ASJ)

AF:

0.599

AC:

1506

AN:

2515

East Asian (EAS)

AF:

0.711

AC:

2198

AN:

3093

South Asian (SAS)

AF:

0.554

AC:

1162

AN:

2097

European-Finnish (FIN)

AF:

0.353

AC:

1610

AN:

4560

Middle Eastern (MID)

AF:

0.602

AC:

124

AN:

206

European-Non Finnish (NFE)

AF:

0.384

AC:

19174

AN:

49993

Other (OTH)

AF:

0.586

AC:

795

AN:

1356

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

767

1533

2300

3066

3833

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.477

Hom.:

3040

Bravo

AF:

0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.35

(source)

DANN

Benign

0.13

PhyloP100

-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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