Genetic Variant ENSG00000294104:n.148+2645T>C (chrX-5478155-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 ENST00000721126.1(ENSG00000294104):n.148+2645T>C 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 0.57 ( 12833 hom., 18388 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

ENSG00000294104
ENST00000721126.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

1 publications found

Variant links:

Genes affected

ENSG00000294104 (HGNC:):

ENSG00000294104 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=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294104	ENST00000721126.1 link	n.148+2645T>C		intron_variant	Intron 1 of 1
ENSG00000294104	ENST00000721127.1 link	n.196+2560T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.571

AC:

62726

AN:

109920

Hom.:

12831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.555

Gnomad AMI

AF:

0.550

Gnomad AMR

AF:

0.722

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.503

Gnomad SAS

AF:

0.577

Gnomad FIN

AF:

0.538

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.581

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:

0.571

AC:

62750

AN:

109968

Hom.:

12833

Cov.:

AF XY:

0.570

AC XY:

18388

AN XY:

32248

show subpopulations

African (AFR)

AF:

0.555

AC:

16836

AN:

30334

American (AMR)

AF:

0.723

AC:

7397

AN:

10237

Ashkenazi Jewish (ASJ)

AF:

0.607

AC:

1598

AN:

2633

East Asian (EAS)

AF:

0.502

AC:

1737

AN:

3458

South Asian (SAS)

AF:

0.578

AC:

1496

AN:

2587

European-Finnish (FIN)

AF:

0.538

AC:

3030

AN:

5632

Middle Eastern (MID)

AF:

0.514

AC:

107

AN:

208

European-Non Finnish (NFE)

AF:

0.556

AC:

29311

AN:

52709

Other (OTH)

AF:

0.580

AC:

868

AN:

1497

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

979

1957

2936

3914

4893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<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:

0.576

Hom.:

5009

Bravo

AF:

0.587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.053

(source)

DANN

Benign

0.40

PhyloP100

-1.4

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over