rs1192844186

Variant names:

• chr14-22981788-T-A
• NM_032876.6:c.479A>T

Your query was ambiguous. Multiple possible variants found:

• chr14-22981788-T-A
• chr14-22981788-T-C
• chr14-22981788-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_032876.6(AJUBA):​c.479A>T​(p.Asn160Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000724 in 1,381,958 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N160S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: AJUBA NM_032876.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

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]

ENSG00000259132 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AJUBA	NM_032876.6	c.479A>T	p.Asn160Ile	missense_variant	Exon 1 of 8	ENST00000262713.7	NP_116265.1
AJUBA	NM_001289097.2	c.479A>T	p.Asn160Ile	missense_variant	Exon 1 of 2		NP_001276026.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AJUBA	ENST00000262713.7	c.479A>T	p.Asn160Ile	missense_variant	Exon 1 of 8	1	NM_032876.6	ENSP00000262713.2
ENSG00000259132	ENST00000555074.1	c.49+421A>T		intron_variant	Intron 1 of 4	2		ENSP00000450856.2
AJUBA	ENST00000553736.1	c.-203A>T		upstream_gene_variant		2		ENSP00000451772.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.24e-7 AC: 1 AN: 1381958 Hom.: 0 Cov.: 31 AF XY: 0.00000147 AC XY: 1 AN XY: 681948

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000398

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Uncertain	0.026	T
BayesDel_noAF	Benign	-0.20
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.31	T;T
Eigen	Benign	0.16
Eigen_PC	Benign	0.21
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.90	.;D
M_CAP	Uncertain	0.21	D
MetaRNN	Uncertain	0.52	D;D
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.5	L;L
PrimateAI	Pathogenic	0.85	D
PROVEAN	Uncertain	-3.4	D;D
REVEL	Benign	0.23
Sift	Pathogenic	0.0	D;D
Sift4G	Benign	0.12	T;T
Polyphen		0.92	P;P
Vest4		0.60
MutPred		0.27		Gain of catalytic residue at P157 (P = 2e-04);Gain of catalytic residue at P157 (P = 2e-04);
MVP		0.70
ClinPred		0.98	D
GERP RS		3.4
Varity_R		0.46
gMVP		0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-23450997;