10-133325897-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015722.4(CALY):c.584C>A(p.Pro195Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000235 in 1,277,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015722.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALY | NM_015722.4 | c.584C>A | p.Pro195Gln | missense_variant | 5/6 | ENST00000252939.9 | |
ZNF511-PRAP1 | NM_001396060.1 | c.680+14056G>T | intron_variant | ||||
CALY | NM_001321617.2 | c.338C>A | p.Pro113Gln | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALY | ENST00000252939.9 | c.584C>A | p.Pro195Gln | missense_variant | 5/6 | 1 | NM_015722.4 | P1 | |
CALY | ENST00000467433.5 | n.279C>A | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
CALY | ENST00000467611.1 | n.418C>A | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
CALY | ENST00000368558.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151980Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000178 AC: 2AN: 1125394Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 537654
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151980Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.584C>A (p.P195Q) alteration is located in exon 5 (coding exon 4) of the CALY gene. This alteration results from a C to A substitution at nucleotide position 584, causing the proline (P) at amino acid position 195 to be replaced by a glutamine (Q). 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