Genetic Variant ENSG00000286888:n.258+3163T>C (chr4-16358948-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 ENST00000782843.1(ENSG00000286888):n.258+3163T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,132 control chromosomes in the GnomAD database, including 6,058 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 0.24 ( 6058 hom., cov: 33)

Consequence

ENSG00000286888
ENST00000782843.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.459

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286888 (HGNC:):

ENSG00000286888 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=-0.62).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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
ENSG00000286888	ENST00000782843.1 link	n.258+3163T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36463

AN:

152014

Hom.:

6049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0512

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.216

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

GnomAD4 genome

AF:

0.240

AC:

36504

AN:

152132

Hom.:

6058

Cov.:

AF XY:

0.234

AC XY:

17377

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.465

AC:

19307

AN:

41490

American (AMR)

AF:

0.173

AC:

2647

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

478

AN:

3466

East Asian (EAS)

AF:

0.0514

AC:

265

AN:

5160

South Asian (SAS)

AF:

0.162

AC:

781

AN:

4820

European-Finnish (FIN)

AF:

0.167

AC:

1769

AN:

10606

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10673

AN:

67974

Other (OTH)

AF:

0.213

AC:

451

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1265

2529

3794

5058

6323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

346

692

1038

1384

1730

<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:

0.222

Hom.:

633

Bravo

AF:

0.251

Asia WGS

AF:

0.105

AC:

368

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

1.6

(source)

DANN

Benign

0.82

PhyloP100

-0.46

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