11-57758411-A-G

Position:

• chr11-57758411-A-G

Variant summary

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

The NR_037646.1(TMX2-CTNND1):​n.346+20743A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,138 control chromosomes in the GnomAD database, including 7,127 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 (7127 hom., cov: 33)
• Consequence: TMX2-CTNND1 NR_037646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

TMX2-CTNND1 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMX2-CTNND1	NR_037646.1	n.346+20743A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNND1	ENST00000524630.5	c.-214+4869A>G		intron_variant		2		P4
CTNND1	ENST00000529919.5	c.-214+5004A>G		intron_variant		5		A1
CTNND1	ENST00000533189.1	c.-14+5004A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43017 AN: 152020 Hom.: 7114 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.229

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: 43040 AN: 152138 Hom.: 7127 Cov.: 33 AF XY: 0.296 AC XY: 22000 AN XY: 74358

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.280

Alfa AF: 0.144 Hom.: 244

Bravo AF: 0.293

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.64

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

LitVar

Other links and lift over

dbSNP: rs501738; hg19: chr11-57525883;