Genetic Variant ENSG00000294393:n.331-1366T>C (chr5-8055148-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000723339.1(ENSG00000294393):n.331-1366T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,170 control chromosomes in the GnomAD database, including 2,103 homozygotes. 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 0.15 ( 2103 hom., cov: 33)

Consequence

ENSG00000294393
ENST00000723339.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.54

Publications

3 publications found

Variant links:

Genes affected

ENSG00000294393 (HGNC:):

ENSG00000294393 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900937	XR_007058684.1 link	n.*214A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294393	ENST00000723339.1 link	n.331-1366T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22747

AN:

152052

Hom.:

2093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.0893

Gnomad EAS

AF:

0.0832

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0875

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

AF:

0.150

AC:

22794

AN:

152170

Hom.:

2103

Cov.:

AF XY:

0.149

AC XY:

11061

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.272

AC:

11259

AN:

41464

American (AMR)

AF:

0.128

AC:

1958

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0893

AC:

310

AN:

3470

East Asian (EAS)

AF:

0.0834

AC:

432

AN:

5182

South Asian (SAS)

AF:

0.112

AC:

541

AN:

4826

European-Finnish (FIN)

AF:

0.0875

AC:

928

AN:

10608

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6932

AN:

68004

Other (OTH)

AF:

0.132

AC:

280

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

966

1932

2899

3865

4831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.111

Hom.:

1579

Bravo

AF:

0.158

Asia WGS

AF:

0.107

AC:

373

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.067

(source)

DANN

Benign

0.51

PhyloP100

-2.5

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