Genetic Variant ENST00000792604.1:n.266-5649G>A (chr9-82836775-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 ENST00000792604.1(ENSG00000303186):n.266-5649G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,926 control chromosomes in the GnomAD database, including 921 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 0.10 ( 921 hom., cov: 32)

Consequence

ENSG00000303186
ENST00000792604.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Publications

0 publications found

Variant links:

Genes affected

ENSG00000303186 (HGNC:):

ENSG00000303186 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=-1.06).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000303186	ENST00000792604.1 link	n.266-5649G>A	intron_variant	Intron 3 of 4
ENSG00000303186	ENST00000792605.1 link	n.113-5649G>A	intron_variant	Intron 1 of 3
ENSG00000303186	ENST00000792606.1 link	n.75-5649G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15833

AN:

151808

Hom.:

919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.0674

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.0987

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0889

Gnomad OTH

AF:

0.108

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

GnomAD4 genome

AF:

0.104

AC:

15861

AN:

151926

Hom.:

921

Cov.:

AF XY:

0.107

AC XY:

7956

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.118

AC:

4909

AN:

41474

American (AMR)

AF:

0.121

AC:

1848

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

374

AN:

3462

East Asian (EAS)

AF:

0.0669

AC:

345

AN:

5154

South Asian (SAS)

AF:

0.198

AC:

954

AN:

4814

European-Finnish (FIN)

AF:

0.0987

AC:

1042

AN:

10560

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0889

AC:

6037

AN:

67922

Other (OTH)

AF:

0.107

AC:

225

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

715

1430

2146

2861

3576

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.0996

Hom.:

109

Bravo

AF:

0.106

Asia WGS

AF:

0.139

AC:

482

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.64

(source)

DANN

Benign

0.76

PhyloP100

-2.5

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