Genetic Variant ENSG00000303910:n.312+26521T>C (chrX-140545365-T-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 ENST00000797998.1(ENSG00000303910):n.312+26521T>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 0.89 ( 31207 hom., 28551 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000303910
ENST00000797998.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.302

Publications

2 publications found

Variant links:

Genes affected

ENSG00000303910 (HGNC:):

ENSG00000303910 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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000303910	ENST00000797998.1 link	n.312+26521T>C	intron_variant	Intron 2 of 2
ENSG00000303910	ENST00000797999.1 link	n.477-3897T>C	intron_variant	Intron 4 of 4
ENSG00000303910	ENST00000798007.1 link	n.284-3897T>C	intron_variant	Intron 3 of 3
ENSG00000303910	ENST00000798008.1 link	n.128-3733T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.892

AC:

97812

AN:

109635

Hom.:

31224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.748

Gnomad AMI

AF:

0.965

Gnomad AMR

AF:

0.951

Gnomad ASJ

AF:

0.962

Gnomad EAS

AF:

0.987

Gnomad SAS

AF:

0.952

Gnomad FIN

AF:

0.954

Gnomad MID

AF:

0.957

Gnomad NFE

AF:

0.942

Gnomad OTH

AF:

0.903

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:

0.892

AC:

97821

AN:

109688

Hom.:

31207

Cov.:

AF XY:

0.894

AC XY:

28551

AN XY:

31926

show subpopulations

African (AFR)

AF:

0.748

AC:

22531

AN:

30128

American (AMR)

AF:

0.951

AC:

9702

AN:

10199

Ashkenazi Jewish (ASJ)

AF:

0.962

AC:

2532

AN:

2631

East Asian (EAS)

AF:

0.987

AC:

3416

AN:

3461

South Asian (SAS)

AF:

0.950

AC:

2343

AN:

2467

European-Finnish (FIN)

AF:

0.954

AC:

5400

AN:

5659

Middle Eastern (MID)

AF:

0.967

AC:

206

AN:

213

European-Non Finnish (NFE)

AF:

0.942

AC:

49692

AN:

52756

Other (OTH)

AF:

0.899

AC:

1345

AN:

1496

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

354

708

1061

1415

1769

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

794

1588

2382

3176

3970

<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:

0.923

Hom.:

107854

Bravo

AF:

0.888

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.2

(source)

DANN

Benign

0.73

PhyloP100

-0.30

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