dbSNP rs1921708: ENSG00000285679:n.1043-41466G>A (chrX-8328098-G-A) – 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 ENST00000659022.1(ENSG00000285679):n.1043-41466G>A 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 0.61 ( 15868 hom., 19886 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

ENSG00000285679
ENST00000659022.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980

Publications

4 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=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107985675	XR_001755782.2 link	n.1985+99693G>A	intron_variant	Intron 2 of 3
LOC107985675	XR_001755783.2 link	n.1986-92989G>A	intron_variant	Intron 2 of 4
LOC107985675	XR_001755784.2 link	n.1985+99693G>A	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285679	ENST00000659022.1 link	n.1043-41466G>A	intron_variant	Intron 2 of 3
ENSG00000285679	ENST00000746116.1 link	n.72-92989G>A	intron_variant	Intron 1 of 4
ENSG00000285679	ENST00000746117.1 link	n.72-97179G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.613

AC:

67652

AN:

110401

Hom.:

15856

Cov.:

show subpopulations

Gnomad AFR

AF:

0.862

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.641

Gnomad ASJ

AF:

0.485

Gnomad EAS

AF:

0.788

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.402

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.487

Gnomad OTH

AF:

0.635

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:

0.613

AC:

67725

AN:

110455

Hom.:

15868

Cov.:

AF XY:

0.608

AC XY:

19886

AN XY:

32713

show subpopulations

African (AFR)

AF:

0.862

AC:

26203

AN:

30400

American (AMR)

AF:

0.642

AC:

6647

AN:

10355

Ashkenazi Jewish (ASJ)

AF:

0.485

AC:

1276

AN:

2630

East Asian (EAS)

AF:

0.789

AC:

2723

AN:

3453

South Asian (SAS)

AF:

0.536

AC:

1394

AN:

2602

European-Finnish (FIN)

AF:

0.402

AC:

2335

AN:

5810

Middle Eastern (MID)

AF:

0.596

AC:

127

AN:

213

European-Non Finnish (NFE)

AF:

0.487

AC:

25726

AN:

52817

Other (OTH)

AF:

0.638

AC:

960

AN:

1504

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

869

1738

2607

3476

4345

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<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:

0.547

Hom.:

19870

Bravo

AF:

0.648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.54

(source)

DANN

Benign

0.47

PhyloP100

-0.098

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