chr20-37860035-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_030877.5(CTNNBL1):c.1529A>T(p.Gln510Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,944 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030877.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNNBL1 | NM_030877.5 | c.1529A>T | p.Gln510Leu | missense_variant, splice_region_variant | 14/16 | ENST00000361383.11 | |
CTNNBL1 | NM_001281495.2 | c.1448A>T | p.Gln483Leu | missense_variant, splice_region_variant | 15/17 | ||
CTNNBL1 | XM_024451947.2 | c.1448A>T | p.Gln483Leu | missense_variant, splice_region_variant | 15/17 | ||
CTNNBL1 | XM_011528917.3 | c.1199A>T | p.Gln400Leu | missense_variant, splice_region_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNNBL1 | ENST00000361383.11 | c.1529A>T | p.Gln510Leu | missense_variant, splice_region_variant | 14/16 | 1 | NM_030877.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251238Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135770
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461808Hom.: 1 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727200
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.1529A>T (p.Q510L) alteration is located in exon 14 (coding exon 14) of the CTNNBL1 gene. This alteration results from a A to T substitution at nucleotide position 1529, causing the glutamine (Q) at amino acid position 510 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