Genetic Variant ENSG00000286072:n.277+17438G>C (chrX-112864517-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000738665.1(ENSG00000286072):n.277+17438G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 110,786 control chromosomes in the GnomAD database, including 5,946 homozygotes. There are 11,380 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 0.35 ( 5946 hom., 11380 hem., cov: 23)

Consequence

ENSG00000286072
ENST00000738665.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.166

Publications

0 publications found

Variant links:

Genes affected

ENSG00000286072 (HGNC:):

ENSG00000286072 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286072	ENST00000738665.1 link	n.277+17438G>C	intron_variant	Intron 2 of 2
ENSG00000286072	ENST00000738666.1 link	n.396+17438G>C	intron_variant	Intron 3 of 3
ENSG00000286072	ENST00000738667.1 link	n.410+17438G>C	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

39043

AN:

110734

Hom.:

5942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.542

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.585

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.336

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

GnomAD4 genome

AF:

0.353

AC:

39069

AN:

110786

Hom.:

5946

Cov.:

AF XY:

0.344

AC XY:

11380

AN XY:

33050

show subpopulations

African (AFR)

AF:

0.542

AC:

16447

AN:

30363

American (AMR)

AF:

0.472

AC:

4914

AN:

10405

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

366

AN:

2638

East Asian (EAS)

AF:

0.584

AC:

2040

AN:

3492

South Asian (SAS)

AF:

0.183

AC:

479

AN:

2620

European-Finnish (FIN)

AF:

0.306

AC:

1802

AN:

5895

Middle Eastern (MID)

AF:

0.218

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.233

AC:

12319

AN:

52977

Other (OTH)

AF:

0.345

AC:

518

AN:

1503

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

815

1630

2446

3261

4076

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.150

Hom.:

720

Bravo

AF:

0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

(source)

DANN

Benign

0.48

PhyloP100

0.17

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