rs372482202
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_013266.4(CTNNA3):c.1007G>T(p.Arg336Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,613,452 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R336C) has been classified as Uncertain significance.
Frequency
Consequence
NM_013266.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNNA3 | NM_013266.4 | c.1007G>T | p.Arg336Leu | missense_variant | 7/18 | ENST00000433211.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNNA3 | ENST00000433211.7 | c.1007G>T | p.Arg336Leu | missense_variant | 7/18 | 1 | NM_013266.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151886Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250928Hom.: 1 AF XY: 0.000184 AC XY: 25AN XY: 135608
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1461448Hom.: 1 Cov.: 31 AF XY: 0.0000756 AC XY: 55AN XY: 727034
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152004Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.1007G>T (p.R336L) alteration is located in exon 7 (coding exon 6) of the CTNNA3 gene. This alteration results from a G to T substitution at nucleotide position 1007, causing the arginine (R) at amino acid position 336 to be replaced by a leucine (L). 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