15-90629519-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022769.5(CRTC3):āc.1253A>Gā(p.Tyr418Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022769.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTC3 | NM_022769.5 | c.1253A>G | p.Tyr418Cys | missense_variant | 11/15 | ENST00000268184.11 | |
CRTC3-AS1 | NR_120372.1 | n.510-9366T>C | intron_variant, non_coding_transcript_variant | ||||
CRTC3 | NM_001042574.3 | c.1253A>G | p.Tyr418Cys | missense_variant | 11/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTC3 | ENST00000268184.11 | c.1253A>G | p.Tyr418Cys | missense_variant | 11/15 | 1 | NM_022769.5 | P3 | |
CRTC3-AS1 | ENST00000559531.1 | n.511-9366T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251298Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135860
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461746Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727142
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.1253A>G (p.Y418C) alteration is located in exon 11 (coding exon 11) of the CRTC3 gene. This alteration results from a A to G substitution at nucleotide position 1253, causing the tyrosine (Y) at amino acid position 418 to be replaced by a cysteine (C). 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