NM_001085458.2:c.-214+1446G>A

Variant names:

• chr11-57763565-G-A
• rs530094
• NM_001085458.2:c.-214+1446G>A

Variant summary

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

The NM_001085458.2(CTNND1):​c.-214+1446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,020 control chromosomes in the GnomAD database, including 7,128 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 0.28 (7128 hom., cov: 32)
• Consequence: CTNND1 NM_001085458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 3 publications found

Genes affected

CTNND1 (HGNC:2515): (catenin delta 1) This gene encodes a member of the Armadillo protein family, which function in adhesion between cells and signal transduction. Multiple translation initiation codons and alternative splicing result in many different isoforms being translated. Not all of the full-length natures of the described transcript variants have been determined. Read-through transcription also exists between this gene and the neighboring upstream thioredoxin-related transmembrane protein 2 (TMX2) gene. [provided by RefSeq, Dec 2010]

ENSG00000254732 (HGNC:):

TMX2-CTNND1 (HGNC:41992): (TMX2-CTNND1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring TMX2 (thioredoxin-related transmembrane protein 2) and CTNND1 (catenin, cadherin-associated protein, delta 1) genes on chromosome 11. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085458.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNND1	NM_001085458.2	MANE Select	c.-214+1446G>A		intron	N/A	NP_001078927.1
	CTNND1	NM_001085459.2		c.-214+1446G>A		intron	N/A	NP_001078928.1
	CTNND1	NM_001331.3		c.-214+1446G>A		intron	N/A	NP_001322.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNND1	ENST00000399050.10	TSL:1 MANE Select	c.-214+1446G>A		intron	N/A	ENSP00000382004.5
	CTNND1	ENST00000361332.8	TSL:1	c.-214+1446G>A		intron	N/A	ENSP00000354823.4
	CTNND1	ENST00000361391.10	TSL:1	c.-214+1446G>A		intron	N/A	ENSP00000354785.6

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43003 AN: 151904 Hom.: 7115 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.283 AC: 43025 AN: 152020 Hom.: 7128 Cov.: 32 AF XY: 0.296 AC XY: 21997 AN XY: 74314

African (AFR) AF: 0.225 AC: 9317 AN: 41448

American (AMR) AF: 0.412 AC: 6290 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3468

East Asian (EAS) AF: 0.785 AC: 4067 AN: 5178

South Asian (SAS) AF: 0.345 AC: 1666 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3517 AN: 10552

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16271 AN: 67982

Other (OTH) AF: 0.280 AC: 591 AN: 2112

Alfa AF: 0.248 Hom.: 817

Bravo AF: 0.293

Asia WGS AF: 0.575 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.7
DANN	Benign	0.72
PhyloP100		0.073
PromoterAI		-0.071	Neutral
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: rs530094; hg19: chr11-57531037;