Genetic Variant ENSG00000299452:n.515+9418T>C (chr18-63099855-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 ENST00000763645.1(ENSG00000299452):n.515+9418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,204 control chromosomes in the GnomAD database, including 9,734 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 0.33 ( 9734 hom., cov: 33)

Consequence

ENSG00000299452
ENST00000763645.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.909

Publications

4 publications found

Variant links:

Genes affected

ENSG00000299452 (HGNC:):

ENSG00000299452 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299452	ENST00000763645.1 link	n.515+9418T>C	intron_variant	Intron 2 of 2
ENSG00000299452	ENST00000763648.1 link	n.498+9418T>C	intron_variant	Intron 2 of 2
ENSG00000299452	ENST00000763649.1 link	n.516-6440T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49537

AN:

152086

Hom.:

9709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.552

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.363

Gnomad EAS

AF:

0.0738

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.288

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

GnomAD4 genome

AF:

0.326

AC:

49605

AN:

152204

Hom.:

9734

Cov.:

AF XY:

0.321

AC XY:

23863

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.552

AC:

22907

AN:

41498

American (AMR)

AF:

0.217

AC:

3319

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.363

AC:

1259

AN:

3470

East Asian (EAS)

AF:

0.0740

AC:

384

AN:

5190

South Asian (SAS)

AF:

0.293

AC:

1413

AN:

4828

European-Finnish (FIN)

AF:

0.238

AC:

2525

AN:

10598

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.247

AC:

16800

AN:

67996

Other (OTH)

AF:

0.289

AC:

610

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1581

3162

4743

6324

7905

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.268

Hom.:

9517

Bravo

AF:

0.332

Asia WGS

AF:

0.181

AC:

631

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

(source)

DANN

Benign

0.46

PhyloP100

0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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