rs6572891

Positions:

• chr14-22978132-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

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]

LOC124903287 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
AJUBA	NM_032876.6	c.1108+212C>T		intron_variant		ENST00000262713.7
LOC124903287	XR_007064076.1	n.275+31G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AJUBA	ENST00000262713.7	c.1108+212C>T		intron_variant		1	NM_032876.6	P1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68762 AN: 151718 Hom.: 16834 Cov.: 30

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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.432

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

LitVar

Other links and lift over

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