chr10-133328015-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_015722.4(CALY):c.136G>A(p.Val46Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000556 in 1,595,858 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015722.4 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALY | NM_015722.4 | c.136G>A | p.Val46Met | missense_variant, splice_region_variant | 3/6 | ENST00000252939.9 | |
ZNF511-PRAP1 | NM_001396060.1 | c.680+16174C>T | intron_variant | ||||
CALY | NM_001321617.2 | c.-271G>A | splice_region_variant, 5_prime_UTR_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALY | ENST00000252939.9 | c.136G>A | p.Val46Met | missense_variant, splice_region_variant | 3/6 | 1 | NM_015722.4 | P1 | |
CALY | ENST00000368555.3 | c.136G>A | p.Val46Met | missense_variant, splice_region_variant | 3/3 | 2 | |||
CALY | ENST00000368558.1 | c.136G>A | p.Val46Met | missense_variant, splice_region_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000650 AC: 99AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000574 AC: 136AN: 236790Hom.: 1 AF XY: 0.000593 AC XY: 76AN XY: 128250
GnomAD4 exome AF: 0.000547 AC: 789AN: 1443534Hom.: 2 Cov.: 26 AF XY: 0.000589 AC XY: 423AN XY: 718260
GnomAD4 genome ? AF: 0.000650 AC: 99AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000456 AC XY: 34AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.136G>A (p.V46M) alteration is located in exon 3 (coding exon 2) of the CALY gene. This alteration results from a G to A substitution at nucleotide position 136, causing the valine (V) at amino acid position 46 to be replaced by a methionine (M). 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