Genetic Variant ENSG00000307210:n.793+5227C>T (chrX-69134987-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000824576.1(ENSG00000307210):n.793+5227C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 109,968 control chromosomes in the GnomAD database, including 6,115 homozygotes. There are 11,668 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 0.36 ( 6115 hom., 11668 hem., cov: 22)

Consequence

ENSG00000307210
ENST00000824576.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Publications

2 publications found

Variant links:

Genes affected

ENSG00000307210 (HGNC:):

ENSG00000307210 links:

Genome browser will be placed here

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985646	XR_001755985.2 link	n.295-988C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000307210	ENST00000824576.1 link	n.793+5227C>T	intron_variant	Intron 4 of 5
ENSG00000307210	ENST00000824577.1 link	n.788-988C>T	intron_variant	Intron 4 of 4
ENSG00000307210	ENST00000824578.1 link	n.388-988C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

39642

AN:

109910

Hom.:

6122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.550

Gnomad EAS

AF:

0.727

Gnomad SAS

AF:

0.685

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.463

Gnomad NFE

AF:

0.443

Gnomad OTH

AF:

0.405

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

GnomAD4 genome

AF:

0.360

AC:

39640

AN:

109968

Hom.:

6115

Cov.:

AF XY:

0.362

AC XY:

11668

AN XY:

32244

show subpopulations

African (AFR)

AF:

0.122

AC:

3697

AN:

30413

American (AMR)

AF:

0.370

AC:

3801

AN:

10274

Ashkenazi Jewish (ASJ)

AF:

0.550

AC:

1442

AN:

2621

East Asian (EAS)

AF:

0.727

AC:

2483

AN:

3417

South Asian (SAS)

AF:

0.688

AC:

1701

AN:

2471

European-Finnish (FIN)

AF:

0.409

AC:

2340

AN:

5717

Middle Eastern (MID)

AF:

0.442

AC:

AN:

208

European-Non Finnish (NFE)

AF:

0.443

AC:

23346

AN:

52676

Other (OTH)

AF:

0.410

AC:

613

AN:

1494

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

825

1650

2474

3299

4124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.425

Hom.:

43417

Bravo

AF:

0.352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

-0.031

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