Genetic Variant ENSG00000286973:n.510-19666T>C (chr15-23805058-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 ENST00000658937.2(ENSG00000286973):n.510-19666T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,048 control chromosomes in the GnomAD database, including 2,357 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 ( 2357 hom., cov: 32)

Consequence

ENSG00000286973
ENST00000658937.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.338

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286973 (HGNC:):

ENSG00000286973 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286973	ENST00000658937.2 link	n.510-19666T>C	intron_variant	Intron 1 of 2
ENSG00000286973	ENST00000844005.1 link	n.601-19666T>C	intron_variant	Intron 2 of 3
ENSG00000286973	ENST00000844006.1 link	n.472-19666T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24656

AN:

150930

Hom.:

2346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0303

Gnomad SAS

AF:

0.0565

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.173

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

GnomAD4 genome

AF:

0.163

AC:

24686

AN:

151048

Hom.:

2357

Cov.:

AF XY:

0.158

AC XY:

11669

AN XY:

73876

show subpopulations

African (AFR)

AF:

0.272

AC:

11267

AN:

41386

American (AMR)

AF:

0.142

AC:

2138

AN:

15094

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

412

AN:

3462

East Asian (EAS)

AF:

0.0306

AC:

158

AN:

5170

South Asian (SAS)

AF:

0.0553

AC:

267

AN:

4832

European-Finnish (FIN)

AF:

0.110

AC:

1168

AN:

10578

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.130

AC:

8747

AN:

67220

Other (OTH)

AF:

0.171

AC:

359

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1009

2018

3027

4036

5045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<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.:

355

Bravo

AF:

0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.93

(source)

DANN

Benign

0.42

PhyloP100

-0.34

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