Genetic Variant ENSG00000286343:n.104+14754C>T (chr13-107883680-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000663056.1(ENSG00000286343):n.104+14754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,052 control chromosomes in the GnomAD database, including 2,053 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 0.16 ( 2053 hom., cov: 32)

Consequence

ENSG00000286343
ENST00000663056.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430

Publications

2 publications found

Variant links:

Genes affected

ENSG00000286343 (HGNC:):

ENSG00000286343 links:

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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=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

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
ENSG00000286343	ENST00000663056.1 link	n.104+14754C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23605

AN:

151934

Hom.:

2050

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.0941

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.139

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

GnomAD4 genome

AF:

0.155

AC:

23617

AN:

152052

Hom.:

2053

Cov.:

AF XY:

0.162

AC XY:

12011

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.157

AC:

6502

AN:

41492

American (AMR)

AF:

0.133

AC:

2029

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0941

AC:

326

AN:

3466

East Asian (EAS)

AF:

0.387

AC:

2001

AN:

5170

South Asian (SAS)

AF:

0.133

AC:

639

AN:

4812

European-Finnish (FIN)

AF:

0.280

AC:

2951

AN:

10542

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8710

AN:

67988

Other (OTH)

AF:

0.138

AC:

291

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1012

2025

3037

4050

5062

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.134

Hom.:

1802

Bravo

AF:

0.148

Asia WGS

AF:

0.220

AC:

763

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.5

(source)

DANN

Benign

0.58

PhyloP100

0.43

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