Genetic Variant ENSG00000305574:n.44-1533A>T (chrX-151534009-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000811741.1(ENSG00000305574):n.44-1533A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 111,872 control chromosomes in the GnomAD database, including 1,030 homozygotes. There are 3,306 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 0.11 ( 1030 hom., 3306 hem., cov: 23)

Consequence

ENSG00000305574
ENST00000811741.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.933

Publications

1 publications found

Variant links:

Genes affected

ENSG00000305574 (HGNC:):

ENSG00000305574 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373367	NR_188661.1 link	n.229-1533A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000305574	ENST00000811741.1 link	n.44-1533A>T	intron_variant	Intron 1 of 3
ENSG00000305574	ENST00000811742.1 link	n.450-1533A>T	intron_variant	Intron 1 of 2
ENSG00000305574	ENST00000811743.1 link	n.97-1533A>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

12109

AN:

111821

Hom.:

1029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.0397

Gnomad AMR

AF:

0.0598

Gnomad ASJ

AF:

0.0627

Gnomad EAS

AF:

0.00927

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0158

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0396

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.108

AC:

12121

AN:

111872

Hom.:

1030

Cov.:

AF XY:

0.0970

AC XY:

3306

AN XY:

34090

show subpopulations

African (AFR)

AF:

0.286

AC:

8768

AN:

30656

American (AMR)

AF:

0.0597

AC:

631

AN:

10569

Ashkenazi Jewish (ASJ)

AF:

0.0627

AC:

166

AN:

2648

East Asian (EAS)

AF:

0.00930

AC:

AN:

3549

South Asian (SAS)

AF:

0.0454

AC:

121

AN:

2667

European-Finnish (FIN)

AF:

0.0158

AC:

AN:

6124

Middle Eastern (MID)

AF:

0.0558

AC:

AN:

215

European-Non Finnish (NFE)

AF:

0.0395

AC:

2105

AN:

53235

Other (OTH)

AF:

0.105

AC:

161

AN:

1529

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

350

700

1051

1401

1751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.00623

Hom.:

Bravo

AF:

0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.9

(source)

DANN

Benign

0.70

PhyloP100

0.93

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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