Genetic Variant ENSG00000302412:n.167-11761A>G (chrX-137340243-A-G) – 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 ENST00000786458.1(ENSG00000302412):n.167-11761A>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 0.84 ( 29000 hom., 27705 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000302412
ENST00000786458.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.37

Publications

0 publications found

Variant links:

Genes affected

ENSG00000302412 (HGNC:):

ENSG00000302412 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=-1.0).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786458.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000302412	ENST00000786458.1	n.167-11761A>G	intron	N/A
ENSG00000302412	ENST00000786459.1	n.207-11761A>G	intron	N/A
ENSG00000302412	ENST00000786460.1	n.232-11761A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.842

AC:

92931

AN:

110435

Hom.:

29019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.523

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.895

Gnomad ASJ

AF:

0.984

Gnomad EAS

AF:

0.752

Gnomad SAS

AF:

0.938

Gnomad FIN

AF:

0.988

Gnomad MID

AF:

0.941

Gnomad NFE

AF:

0.988

Gnomad OTH

AF:

0.868

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:

0.841

AC:

92951

AN:

110492

Hom.:

29000

Cov.:

AF XY:

0.846

AC XY:

27705

AN XY:

32734

show subpopulations

African (AFR)

AF:

0.523

AC:

15871

AN:

30353

American (AMR)

AF:

0.894

AC:

9301

AN:

10403

Ashkenazi Jewish (ASJ)

AF:

0.984

AC:

2596

AN:

2637

East Asian (EAS)

AF:

0.752

AC:

2573

AN:

3423

South Asian (SAS)

AF:

0.938

AC:

2395

AN:

2552

European-Finnish (FIN)

AF:

0.988

AC:

5783

AN:

5854

Middle Eastern (MID)

AF:

0.940

AC:

203

AN:

216

European-Non Finnish (NFE)

AF:

0.988

AC:

52244

AN:

52867

Other (OTH)

AF:

0.867

AC:

1305

AN:

1506

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

373

745

1118

1490

1863

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<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:

0.920

Hom.:

40303

Bravo

AF:

0.821

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.12

(source)

DANN

Benign

0.70

PhyloP100

-4.4

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over