dbSNP rs10521669: 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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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