rs2180834

Variant names:

• chr14-22971195-G-A
• rs2180834
• NM_032876.6:c.*2248C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-22971195-G-A
• chr14-22971195-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032876.6(AJUBA):​c.*2248C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 151,460 control chromosomes in the GnomAD database, including 4,063 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 0.23 (4063 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: AJUBA NM_032876.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.969
• Publications: 13 publications found

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

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 = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032876.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AJUBA	NM_032876.6	MANE Select	c.*2248C>T		3_prime_UTR	Exon 8 of 8	NP_116265.1
	AJUBA	NM_198086.3		c.*2248C>T		3_prime_UTR	Exon 6 of 6	NP_932352.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AJUBA	ENST00000262713.7	TSL:1 MANE Select	c.*2248C>T		3_prime_UTR	Exon 8 of 8	ENSP00000262713.2
	ENSG00000259132	ENST00000555074.1	TSL:2	c.49+11014C>T		intron	N/A	ENSP00000450856.2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34337 AN: 151348 Hom.: 4059 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.228

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.227 AC: 34367 AN: 151460 Hom.: 4063 Cov.: 31 AF XY: 0.225 AC XY: 16648 AN XY: 73972

African (AFR) AF: 0.254 AC: 10469 AN: 41174

American (AMR) AF: 0.204 AC: 3104 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3470

East Asian (EAS) AF: 0.0465 AC: 240 AN: 5162

South Asian (SAS) AF: 0.124 AC: 594 AN: 4806

European-Finnish (FIN) AF: 0.283 AC: 2932 AN: 10364

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15411 AN: 67958

Other (OTH) AF: 0.234 AC: 492 AN: 2106

Alfa AF: 0.224 Hom.: 15133

Bravo AF: 0.223

Asia WGS AF: 0.146 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.33
PhyloP100		0.97
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2180834; hg19: chr14-23440404;