dbSNP rs10521669: ENSG00000285679:n.144-10006G>C (chrX-8088051-G-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -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

Variant links:

Genes affected

ENSG00000285679 (HGNC:):

ENSG00000285679 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -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.:

AF XY:

0.765

AC XY:

24302

AN XY:

31761

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

Gnomad4 AFR

AF:

0.910

Gnomad4 AMR

AF:

0.818

Gnomad4 ASJ

AF:

0.671

Gnomad4 EAS

AF:

0.928

Gnomad4 SAS

AF:

0.683

Gnomad4 FIN

AF:

0.683

Gnomad4 NFE

AF:

0.692

Gnomad4 OTH

AF:

0.765

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

DANN

Benign

0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over