chr11-57795728-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_001085458.2(CTNND1):c.419C>T(p.Thr140Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000943 in 1,589,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001085458.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNND1 | NM_001085458.2 | c.419C>T | p.Thr140Met | missense_variant, splice_region_variant | 5/21 | ENST00000399050.10 | |
TMX2-CTNND1 | NR_037646.1 | n.978C>T | splice_region_variant, non_coding_transcript_exon_variant | 6/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNND1 | ENST00000399050.10 | c.419C>T | p.Thr140Met | missense_variant, splice_region_variant | 5/21 | 1 | NM_001085458.2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152032Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000322 AC: 7AN: 217404Hom.: 0 AF XY: 0.0000169 AC XY: 2AN XY: 118430
GnomAD4 exome AF: 0.0000876 AC: 126AN: 1437844Hom.: 0 Cov.: 31 AF XY: 0.0000769 AC XY: 55AN XY: 714752
GnomAD4 genome AF: 0.000158 AC: 24AN: 152032Hom.: 0 Cov.: 31 AF XY: 0.000162 AC XY: 12AN XY: 74240
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2023 | The c.419C>T (p.T140M) alteration is located in exon 5 (coding exon 3) of the CTNND1 gene. This alteration results from a C to T substitution at nucleotide position 419, causing the threonine (T) at amino acid position 140 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at