dbSNP rs8088739: 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

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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