Genetic Variant ENSG00000285679:n.144-10006G>C (chrX-8088051-G-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 ENST00000649338.1(ENSG00000285679):n.144-10006G>C 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 0.77 ( 23678 hom., 24354 hem., cov: 21)

Failed GnomAD Quality Control

Consequence

ENSG00000285679
ENST00000649338.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69

Publications

0 publications found

Variant links:

Genes affected

ENSG00000285679 (HGNC:):

ENSG00000285679 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=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107985675	XR_001755782.2 link	n.1915-140284G>C	intron_variant	Intron 1 of 3
LOC107985675	XR_001755783.2 link	n.1915-140284G>C	intron_variant	Intron 1 of 4
LOC107985675	XR_001755784.2 link	n.1915-140284G>C	intron_variant	Intron 1 of 4
LOC107985675	XR_007068387.1 link	n.1915-140284G>C	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285679	ENST00000649338.1 link	n.144-10006G>C		intron_variant	Intron 2 of 4
ENSG00000285679	ENST00000659022.1 link	n.972-140284G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.771

AC:

84385

AN:

109495

Hom.:

23675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.910

Gnomad AMI

AF:

0.617

Gnomad AMR

AF:

0.817

Gnomad ASJ

AF:

0.671

Gnomad EAS

AF:

0.927

Gnomad SAS

AF:

0.682

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.692

Gnomad OTH

AF:

0.769

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:

0.771

AC:

84444

AN:

109545

Hom.:

23678

Cov.:

AF XY:

0.765

AC XY:

24354

AN XY:

31821

show subpopulations

African (AFR)

AF:

0.910

AC:

27479

AN:

30183

American (AMR)

AF:

0.818

AC:

8373

AN:

10242

Ashkenazi Jewish (ASJ)

AF:

0.671

AC:

1752

AN:

2611

East Asian (EAS)

AF:

0.928

AC:

3162

AN:

3409

South Asian (SAS)

AF:

0.683

AC:

1693

AN:

2479

European-Finnish (FIN)

AF:

0.683

AC:

3892

AN:

5700

Middle Eastern (MID)

AF:

0.728

AC:

150

AN:

206

European-Non Finnish (NFE)

AF:

0.692

AC:

36389

AN:

52554

Other (OTH)

AF:

0.765

AC:

1142

AN:

1493

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

657

1314

1971

2628

3285

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<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:

0.743

Hom.:

6140

Bravo

AF:

0.790

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.26

(source)

DANN

Benign

0.44

PhyloP100

-1.7

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