Genetic Variant ENST00000790756.1:n.183C>T (chrX-115345861-C-T) – 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 ENST00000790756.1(ENSG00000302967):n.183C>T variant causes a non coding transcript exon 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 ( 27540 hom., 27573 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000302967
ENST00000790756.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.607

Publications

1 publications found

Variant links:

Genes affected

ENSG00000302967 (HGNC:):

ENSG00000302967 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=-0.77).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790756.1. 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302967	ENST00000790756.1		n.183C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000302967	ENST00000790757.1		n.90+156C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.843

AC:

92912

AN:

110171

Hom.:

27542

Cov.:

show subpopulations

Gnomad AFR

AF:

0.852

Gnomad AMI

AF:

0.871

Gnomad AMR

AF:

0.867

Gnomad ASJ

AF:

0.791

Gnomad EAS

AF:

0.948

Gnomad SAS

AF:

0.947

Gnomad FIN

AF:

0.874

Gnomad MID

AF:

0.845

Gnomad NFE

AF:

0.821

Gnomad OTH

AF:

0.848

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:

0.843

AC:

92959

AN:

110224

Hom.:

27540

Cov.:

AF XY:

0.850

AC XY:

27573

AN XY:

32452

show subpopulations

African (AFR)

AF:

0.851

AC:

25777

AN:

30274

American (AMR)

AF:

0.867

AC:

8993

AN:

10373

Ashkenazi Jewish (ASJ)

AF:

0.791

AC:

2080

AN:

2629

East Asian (EAS)

AF:

0.948

AC:

3303

AN:

3486

South Asian (SAS)

AF:

0.948

AC:

2402

AN:

2533

European-Finnish (FIN)

AF:

0.874

AC:

5041

AN:

5768

Middle Eastern (MID)

AF:

0.850

AC:

181

AN:

213

European-Non Finnish (NFE)

AF:

0.821

AC:

43328

AN:

52784

Other (OTH)

AF:

0.850

AC:

1273

AN:

1497

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

535

1071

1606

2142

2677

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

770

1540

2310

3080

3850

<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:

0.833

Hom.:

8143

Bravo

AF:

0.846

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

6.4

(source)

PhyloP100

0.61

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