chr14-22978132-G-A

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

2

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

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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
AJUBANM_032876.6 linkc.1108+212C>T intron_variant Intron 2 of 7 ENST00000262713.7 NP_116265.1 Q96IF1-1
LOC124903287XR_007064076.1 linkn.275+31G>A intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AJUBAENST00000262713.7 linkc.1108+212C>T intron_variant Intron 2 of 7 1 NM_032876.6 ENSP00000262713.2 Q96IF1-1
ENSG00000259132ENST00000555074.1 linkc.49+4077C>T intron_variant Intron 1 of 4 2 ENSP00000450856.2 G3V2T6
AJUBA-DTENST00000723391.1 linkn.75+79G>A intron_variant Intron 1 of 3
AJUBA-DTENST00000723408.1 linkn.47+79G>A intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.453
AC:
68762
AN:
151718
Hom.:
16834
Cov.:
30
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.:
30
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
0
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
0
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
DANN
Benign
0.77
PhyloP100
-0.48
PromoterAI
-0.016
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs6572891; hg19: chr14-23447341; COSMIC: COSV52985532; COSMIC: COSV52985532; API