rs556623128
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_013266.4(CTNNA3):c.1959C>T(p.Thr653=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,613,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T653T) has been classified as Likely benign.
Frequency
Consequence
NM_013266.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNNA3 | NM_013266.4 | c.1959C>T | p.Thr653= | synonymous_variant | 14/18 | ENST00000433211.7 | |
LOC105378340 | XR_007062172.1 | n.226+4358G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNNA3 | ENST00000433211.7 | c.1959C>T | p.Thr653= | synonymous_variant | 14/18 | 1 | NM_013266.4 | P1 | |
ENST00000608793.1 | n.485+4358G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251384Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135856
GnomAD4 exome AF: 0.0000800 AC: 117AN: 1461604Hom.: 0 Cov.: 30 AF XY: 0.0000921 AC XY: 67AN XY: 727138
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Arrhythmogenic right ventricular dysplasia 13 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 25, 2022 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 03, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at