7-71810387-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_031468.4(CALN1):c.607G>A(p.Glu203Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,022 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_031468.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CALN1 | ENST00000395275.7 | c.607G>A | p.Glu203Lys | missense_variant | Exon 6 of 7 | 5 | NM_031468.4 | ENSP00000378690.2 | ||
CALN1 | ENST00000329008.9 | c.481G>A | p.Glu161Lys | missense_variant | Exon 5 of 6 | 1 | ENSP00000332498.5 | |||
CALN1 | ENST00000395276.6 | c.481G>A | p.Glu161Lys | missense_variant | Exon 6 of 7 | 1 | ENSP00000378691.2 | |||
CALN1 | ENST00000431984.5 | c.481G>A | p.Glu161Lys | missense_variant | Exon 5 of 6 | 1 | ENSP00000410704.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251422Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727214
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.607G>A (p.E203K) alteration is located in exon 6 (coding exon 5) of the CALN1 gene. This alteration results from a G to A substitution at nucleotide position 607, causing the glutamic acid (E) at amino acid position 203 to be replaced by a lysine (K). 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