Genetic Variant ENSG00000286147:n.102-17633C>T (chr4-106602743-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 ENST00000650850.1(ENSG00000286147):n.102-17633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.071 in 151,852 control chromosomes in the GnomAD database, including 505 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 0.071 ( 505 hom., cov: 31)

Consequence

ENSG00000286147
ENST00000650850.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.307

Publications

3 publications found

Variant links:

Genes affected

ENSG00000286147 (HGNC:):

ENSG00000286147 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377356	XR_939051.1 link	n.94-24291C>T		intron_variant	Intron 1 of 5
LOC105377356	XR_939053.3 link	n.94-24291C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286147	ENST00000650850.1 link	n.102-17633C>T		intron_variant	Intron 1 of 10

Frequencies

GnomAD3 genomes

AF:

0.0710

AC:

10770

AN:

151734

Hom.:

504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0732

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0531

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.0654

Gnomad FIN

AF:

0.0917

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0551

Gnomad OTH

AF:

0.0598

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

GnomAD4 genome

AF:

0.0710

AC:

10784

AN:

151852

Hom.:

505

Cov.:

AF XY:

0.0743

AC XY:

5513

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.0731

AC:

3026

AN:

41418

American (AMR)

AF:

0.123

AC:

1866

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.0531

AC:

184

AN:

3468

East Asian (EAS)

AF:

0.104

AC:

538

AN:

5162

South Asian (SAS)

AF:

0.0658

AC:

317

AN:

4816

European-Finnish (FIN)

AF:

0.0917

AC:

963

AN:

10496

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0551

AC:

3742

AN:

67952

Other (OTH)

AF:

0.0592

AC:

125

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

499

998

1496

1995

2494

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0581

Hom.:

221

Bravo

AF:

0.0746

Asia WGS

AF:

0.0950

AC:

331

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.9

(source)

DANN

Benign

0.44

PhyloP100

-0.31

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