Genetic Variant ENST00000422438.5:n.161-374T>G (chrX-16153837-A-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 ENST00000422438.5(MAGEB17-AS1):n.161-374T>G 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 0.64 ( 16237 hom., 20551 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

MAGEB17-AS1
ENST00000422438.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Publications

2 publications found

Variant links:

Genes affected

MAGEB17-AS1 (HGNC:56739): (MAGEB17 antisense RNA 1)

MAGEB17-AS1 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=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGEB17-AS1	NR_187144.1 link	n.1707-374T>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MAGEB17-AS1	ENST00000422438.5 link	n.161-374T>G	intron_variant	Intron 2 of 3	3
MAGEB17-AS1	ENST00000435789.1 link	n.794-374T>G	intron_variant	Intron 5 of 5	5
MAGEB17-AS1	ENST00000454712.8 link	n.704-374T>G	intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

70234

AN:

110365

Hom.:

16234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.778

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.630

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.547

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.613

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:

0.636

AC:

70279

AN:

110418

Hom.:

16237

Cov.:

AF XY:

0.629

AC XY:

20551

AN XY:

32694

show subpopulations

African (AFR)

AF:

0.778

AC:

23593

AN:

30317

American (AMR)

AF:

0.629

AC:

6569

AN:

10446

Ashkenazi Jewish (ASJ)

AF:

0.544

AC:

1431

AN:

2629

East Asian (EAS)

AF:

0.697

AC:

2438

AN:

3496

South Asian (SAS)

AF:

0.565

AC:

1476

AN:

2613

European-Finnish (FIN)

AF:

0.547

AC:

3155

AN:

5768

Middle Eastern (MID)

AF:

0.546

AC:

119

AN:

218

European-Non Finnish (NFE)

AF:

0.573

AC:

30232

AN:

52767

Other (OTH)

AF:

0.612

AC:

912

AN:

1490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

895

1789

2684

3578

4473

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.591

Hom.:

55570

Bravo

AF:

0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

1.2

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