Genetic Variant AJUBA:c.1108+212C>T (chr14-22978132-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 NM_032876.6(AJUBA):c.1108+212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,836 control chromosomes in the GnomAD database, including 16,866 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 0.45 ( 16866 hom., cov: 30)

Consequence

AJUBA
NM_032876.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.485

Publications

12 publications found

Variant links:

Genes affected

AJUBA (HGNC:20250): (ajuba LIM protein) Enables alpha-catenin binding activity and transcription corepressor activity. Involved in several processes, including negative regulation of hippo signaling; positive regulation of gene silencing by miRNA; and regulation of cellular response to hypoxia. Acts upstream of or within gene silencing by miRNA and positive regulation of protein-containing complex assembly. Located in several cellular components, including Golgi apparatus; P-body; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

AJUBA links:

ENSG00000259132 (HGNC:):

ENSG00000259132 links:

AJUBA-DT (HGNC:55449): (AJUBA divergent transcript)

AJUBA-DT 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AJUBA	NM_032876.6 link	c.1108+212C>T		intron_variant	Intron 2 of 7	ENST00000262713.7	NP_116265.1	Q96IF1-1
LOC124903287	XR_007064076.1 link	n.275+31G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
AJUBA	ENST00000262713.7 link	c.1108+212C>T	intron_variant	Intron 2 of 7	1	NM_032876.6	ENSP00000262713.2	Q96IF1-1
ENSG00000259132	ENST00000555074.1 link	c.49+4077C>T	intron_variant	Intron 1 of 4	2		ENSP00000450856.2	G3V2T6
AJUBA-DT	ENST00000723391.1 link	n.75+79G>A	intron_variant	Intron 1 of 3
AJUBA-DT	ENST00000723408.1 link	n.47+79G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.453

AC:

68762

AN:

151718

Hom.:

16834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.638

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.413

Gnomad ASJ

AF:

0.421

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.344

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.426

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

GnomAD4 genome

AF:

0.453

AC:

68836

AN:

151836

Hom.:

16866

Cov.:

AF XY:

0.449

AC XY:

33308

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.638

AC:

26407

AN:

41388

American (AMR)

AF:

0.413

AC:

6308

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.421

AC:

1462

AN:

3470

East Asian (EAS)

AF:

0.206

AC:

1060

AN:

5144

South Asian (SAS)

AF:

0.253

AC:

1217

AN:

4808

European-Finnish (FIN)

AF:

0.419

AC:

4421

AN:

10544

Middle Eastern (MID)

AF:

0.349

AC:

102

AN:

292

European-Non Finnish (NFE)

AF:

0.394

AC:

26721

AN:

67906

Other (OTH)

AF:

0.432

AC:

908

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1780

3560

5339

7119

8899

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<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:

0.431

Hom.:

2367

Bravo

AF:

0.461

Asia WGS

AF:

0.286

AC:

997

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.8

(source)

DANN

Benign

0.77

PhyloP100

-0.48

PromoterAI

-0.016

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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