15-90629434-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022769.5(CRTC3):c.1168G>A(p.Val390Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000626 in 1,613,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022769.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRTC3 | NM_022769.5 | c.1168G>A | p.Val390Ile | missense_variant | Exon 11 of 15 | ENST00000268184.11 | NP_073606.3 | |
CRTC3 | NM_001042574.3 | c.1168G>A | p.Val390Ile | missense_variant | Exon 11 of 15 | NP_001036039.1 | ||
CRTC3-AS1 | NR_120372.1 | n.510-9281C>T | intron_variant | Intron 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRTC3 | ENST00000268184.11 | c.1168G>A | p.Val390Ile | missense_variant | Exon 11 of 15 | 1 | NM_022769.5 | ENSP00000268184.6 | ||
CRTC3 | ENST00000420329.6 | c.1168G>A | p.Val390Ile | missense_variant | Exon 11 of 15 | 2 | ENSP00000416573.2 | |||
CRTC3 | ENST00000686240.1 | n.*581G>A | non_coding_transcript_exon_variant | Exon 10 of 14 | ENSP00000508866.1 | |||||
CRTC3 | ENST00000691029.1 | n.1168G>A | non_coding_transcript_exon_variant | Exon 11 of 17 | ENSP00000510507.1 | |||||
CRTC3 | ENST00000692149.1 | n.*495G>A | non_coding_transcript_exon_variant | Exon 9 of 13 | ENSP00000510448.1 | |||||
CRTC3 | ENST00000686240.1 | n.*581G>A | 3_prime_UTR_variant | Exon 10 of 14 | ENSP00000508866.1 | |||||
CRTC3 | ENST00000692149.1 | n.*495G>A | 3_prime_UTR_variant | Exon 9 of 13 | ENSP00000510448.1 | |||||
CRTC3 | ENST00000687075.1 | n.*404G>A | downstream_gene_variant | ENSP00000510590.1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 151910Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251424Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135900
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.0000578 AC XY: 42AN XY: 727234
GnomAD4 genome AF: 0.000204 AC: 31AN: 151910Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74186
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1168G>A (p.V390I) alteration is located in exon 11 (coding exon 11) of the CRTC3 gene. This alteration results from a G to A substitution at nucleotide position 1168, causing the valine (V) at amino acid position 390 to be replaced by an isoleucine (I). 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