19-12940336-T-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004343.4(CALR):c.586T>G(p.Leu196Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004343.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CALR | NM_004343.4 | c.586T>G | p.Leu196Val | missense_variant | Exon 5 of 9 | ENST00000316448.10 | NP_004334.1 | |
MIR6515 | NR_106770.1 | n.-148T>G | upstream_gene_variant | |||||
MIR6515 | unassigned_transcript_3232 | n.-150T>G | upstream_gene_variant | |||||
MIR6515 | unassigned_transcript_3233 | n.-185T>G | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251492Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135920
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461880Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727246
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.586T>G (p.L196V) alteration is located in exon 5 (coding exon 5) of the CALR gene. This alteration results from a T to G substitution at nucleotide position 586, causing the leucine (L) at amino acid position 196 to be replaced by a valine (V). 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