Genetic Variant ENST00000786109.1:n.394+1155G>A (chr11-15902016-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000786109.1(ENSG00000289116):n.394+1155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,194 control chromosomes in the GnomAD database, including 10,199 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 ( 10199 hom., cov: 34)

Consequence

ENSG00000289116
ENST00000786109.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.134

Publications

9 publications found

Variant links:

Genes affected

ENSG00000289116 (HGNC:):

ENSG00000289116 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) 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
ENSG00000289116	ENST00000786109.1 link	n.394+1155G>A		intron_variant	Intron 2 of 2
ENSG00000302370	ENST00000786200.1 link	n.-135C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50479

AN:

152076

Hom.:

10204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.545

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.00673

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.362

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

GnomAD4 genome

AF:

0.332

AC:

50467

AN:

152194

Hom.:

10199

Cov.:

AF XY:

0.328

AC XY:

24382

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.132

AC:

5485

AN:

41530

American (AMR)

AF:

0.298

AC:

4560

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.441

AC:

1532

AN:

3470

East Asian (EAS)

AF:

0.00694

AC:

AN:

5190

South Asian (SAS)

AF:

0.274

AC:

1321

AN:

4826

European-Finnish (FIN)

AF:

0.430

AC:

4549

AN:

10578

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.465

AC:

31603

AN:

67996

Other (OTH)

AF:

0.360

AC:

761

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1614

3228

4843

6457

8071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<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:

0.418

Hom.:

24383

Bravo

AF:

0.313

Asia WGS

AF:

0.163

AC:

570

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.53

(source)

DANN

Benign

0.90

PhyloP100

-0.13

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