Genetic Variant ENST00000655229.1:n.43-11076C>T (chr13-80997555-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 ENST00000655229.1(ENSG00000286746):n.43-11076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,038 control chromosomes in the GnomAD database, including 7,324 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 0.29 ( 7324 hom., cov: 32)

Consequence

ENSG00000286746
ENST00000655229.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.90

Publications

3 publications found

Variant links:

Genes affected

ENSG00000286746 (HGNC:):

ENSG00000286746 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=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286746	ENST00000655229.1 link	n.43-11076C>T	intron_variant	Intron 1 of 1
ENSG00000286746	ENST00000660876.1 link	n.53+20125C>T	intron_variant	Intron 1 of 1
ENSG00000286746	ENST00000661648.1 link	n.30+20125C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43510

AN:

151916

Hom.:

7325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.277

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.334

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

GnomAD4 genome

AF:

0.286

AC:

43518

AN:

152038

Hom.:

7324

Cov.:

AF XY:

0.295

AC XY:

21909

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.128

AC:

5299

AN:

41484

American (AMR)

AF:

0.276

AC:

4224

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1234

AN:

3472

East Asian (EAS)

AF:

0.232

AC:

1196

AN:

5154

South Asian (SAS)

AF:

0.299

AC:

1442

AN:

4828

European-Finnish (FIN)

AF:

0.537

AC:

5664

AN:

10542

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.345

AC:

23470

AN:

67962

Other (OTH)

AF:

0.336

AC:

710

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1514

3029

4543

6058

7572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.337

Hom.:

13610

Bravo

AF:

0.260

Asia WGS

AF:

0.257

AC:

892

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.098

(source)

DANN

Benign

0.22

PhyloP100

-1.9

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