Genetic Variant ENSG00000285899:n.619-11322T>C (chrX-43427013-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000649774.1(ENSG00000285899):n.619-11322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 111,952 control chromosomes in the GnomAD database, including 41 homozygotes. There are 691 hemizygotes in GnomAD. 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 0.021 ( 41 hom., 691 hem., cov: 23)

Consequence

ENSG00000285899
ENST00000649774.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.155

Publications

0 publications found

Variant links:

Genes affected

ENSG00000285899 (HGNC:):

ENSG00000285899 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.066 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285899	ENST00000649774.1 link	n.619-11322T>C	intron_variant	Intron 7 of 7
ENSG00000285899	ENST00000811237.1 link	n.298-11322T>C	intron_variant	Intron 3 of 3
ENSG00000285899	ENST00000811238.1 link	n.363-11322T>C	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0209

AC:

2335

AN:

111895

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00426

Gnomad AMI

AF:

0.00291

Gnomad AMR

AF:

0.0699

Gnomad ASJ

AF:

0.0238

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00862

Gnomad FIN

AF:

0.0307

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0217

Gnomad OTH

AF:

0.0239

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0209

AC:

2340

AN:

111952

Hom.:

Cov.:

AF XY:

0.0203

AC XY:

691

AN XY:

34120

show subpopulations

African (AFR)

AF:

0.00425

AC:

131

AN:

30852

American (AMR)

AF:

0.0702

AC:

742

AN:

10577

Ashkenazi Jewish (ASJ)

AF:

0.0238

AC:

AN:

2643

East Asian (EAS)

AF:

0.00

AC:

AN:

3537

South Asian (SAS)

AF:

0.00901

AC:

AN:

2663

European-Finnish (FIN)

AF:

0.0307

AC:

188

AN:

6125

Middle Eastern (MID)

AF:

0.00

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.0217

AC:

1154

AN:

53127

Other (OTH)

AF:

0.0236

AC:

AN:

1524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

159

238

318

397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<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:

0.0241

Hom.:

203

Bravo

AF:

0.0251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

3.3

(source)

DANN

Benign

0.82

PhyloP100

0.15

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