Genetic Variant ENST00000746116.1:n.225-540C>A (chrX-8439288-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000746116.1(ENSG00000285679):n.225-540C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 109,562 control chromosomes in the GnomAD database, including 3,018 homozygotes. There are 8,256 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 0.27 ( 3018 hom., 8256 hem., cov: 22)

Consequence

ENSG00000285679
ENST00000746116.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.241

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285679 (HGNC:):

ENSG00000285679 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107985675	XR_001755782.2 link	n.1986-540C>A	intron_variant	Intron 2 of 3
LOC107985675	XR_001755783.2 link	n.6226-540C>A	intron_variant	Intron 3 of 4
LOC107985675	XR_001755784.2 link	n.1986-540C>A	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285679	ENST00000746116.1 link	n.225-540C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

29731

AN:

109513

Hom.:

3020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.293

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

GnomAD4 genome

AF:

0.271

AC:

29731

AN:

109562

Hom.:

3018

Cov.:

AF XY:

0.259

AC XY:

8256

AN XY:

31858

show subpopulations

African (AFR)

AF:

0.214

AC:

6472

AN:

30245

American (AMR)

AF:

0.354

AC:

3588

AN:

10131

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

912

AN:

2633

East Asian (EAS)

AF:

0.189

AC:

658

AN:

3479

South Asian (SAS)

AF:

0.196

AC:

501

AN:

2560

European-Finnish (FIN)

AF:

0.231

AC:

1297

AN:

5622

Middle Eastern (MID)

AF:

0.393

AC:

AN:

211

European-Non Finnish (NFE)

AF:

0.295

AC:

15507

AN:

52528

Other (OTH)

AF:

0.289

AC:

429

AN:

1482

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

809

1618

2427

3236

4045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

302

604

906

1208

1510

<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:

0.267

Hom.:

8317

Bravo

AF:

0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.1

(source)

DANN

Benign

0.43

PhyloP100

-0.24

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