Genetic Variant ENSG00000286072:n.347-37088G>T (chrX-113174337-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 ENST00000651919.1(ENSG00000286072):n.347-37088G>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 0.73 ( 21680 hom., 23822 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

ENSG00000286072
ENST00000651919.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.899

Publications

1 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: 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
LOC101928437	NR_110399.2 link	n.231+62272G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286072	ENST00000651919.1 link	n.347-37088G>T		intron_variant	Intron 5 of 5
ENSG00000286767	ENST00000663700.2 link	n.74-12986G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.732

AC:

81050

AN:

110715

Hom.:

21680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.907

Gnomad AMI

AF:

0.578

Gnomad AMR

AF:

0.692

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.741

Gnomad SAS

AF:

0.642

Gnomad FIN

AF:

0.625

Gnomad MID

AF:

0.746

Gnomad NFE

AF:

0.663

Gnomad OTH

AF:

0.725

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:

0.732

AC:

81104

AN:

110769

Hom.:

21680

Cov.:

AF XY:

0.722

AC XY:

23822

AN XY:

33001

show subpopulations

African (AFR)

AF:

0.907

AC:

27749

AN:

30600

American (AMR)

AF:

0.692

AC:

7172

AN:

10368

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

1612

AN:

2635

East Asian (EAS)

AF:

0.741

AC:

2602

AN:

3512

South Asian (SAS)

AF:

0.641

AC:

1704

AN:

2659

European-Finnish (FIN)

AF:

0.625

AC:

3634

AN:

5813

Middle Eastern (MID)

AF:

0.749

AC:

161

AN:

215

European-Non Finnish (NFE)

AF:

0.663

AC:

34984

AN:

52786

Other (OTH)

AF:

0.727

AC:

1098

AN:

1510

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

759

1517

2276

3034

3793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

692

1384

2076

2768

3460

<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:

0.704

Hom.:

5833

Bravo

AF:

0.744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.46

(source)

DANN

Benign

0.16

PhyloP100

-0.90

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