dbSNP rs7892812: ENSG00000285679:n.224+886A>G (chrX-8426212-A-G) – 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 ENST00000746116.1(ENSG00000285679):n.224+886A>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 0.59 ( 14363 hom., 18260 hem., cov: 21)

Failed GnomAD Quality Control

Consequence

ENSG00000285679
ENST00000746116.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.502

Publications

3 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=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107985675	XR_001755782.2 link	n.1986-13616A>G	intron_variant	Intron 2 of 3
LOC107985675	XR_001755783.2 link	n.6225+886A>G	intron_variant	Intron 3 of 4
LOC107985675	XR_001755784.2 link	n.1986-13616A>G	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285679	ENST00000746116.1 link	n.224+886A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.595

AC:

64807

AN:

108972

Hom.:

14364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.744

Gnomad AMI

AF:

0.637

Gnomad AMR

AF:

0.649

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.669

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.505

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.516

Gnomad OTH

AF:

0.591

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:

0.595

AC:

64860

AN:

109031

Hom.:

14363

Cov.:

AF XY:

0.582

AC XY:

18260

AN XY:

31373

show subpopulations

African (AFR)

AF:

0.744

AC:

22284

AN:

29949

American (AMR)

AF:

0.648

AC:

6537

AN:

10089

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

1309

AN:

2622

East Asian (EAS)

AF:

0.669

AC:

2273

AN:

3397

South Asian (SAS)

AF:

0.452

AC:

1132

AN:

2506

European-Finnish (FIN)

AF:

0.505

AC:

2866

AN:

5670

Middle Eastern (MID)

AF:

0.557

AC:

117

AN:

210

European-Non Finnish (NFE)

AF:

0.516

AC:

27039

AN:

52441

Other (OTH)

AF:

0.593

AC:

881

AN:

1485

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

907

1814

2720

3627

4534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

566

1132

1698

2264

2830

<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:

0.552

Hom.:

80457

Bravo

AF:

0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.4

(source)

DANN

Benign

0.22

PhyloP100

-0.50

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