10-133328970-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015722.4(CALY):c.20G>T(p.Ser7Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000708 in 1,412,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CALY | NM_015722.4 | c.20G>T | p.Ser7Ile | missense_variant | Exon 2 of 6 | ENST00000252939.9 | NP_056537.1 | |
CALY | NM_001321617.2 | c.-387G>T | 5_prime_UTR_variant | Exon 2 of 6 | NP_001308546.1 | |||
ZNF511-PRAP1 | NM_001396060.1 | c.680+17129C>A | intron_variant | Intron 5 of 8 | NP_001382989.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CALY | ENST00000252939.9 | c.20G>T | p.Ser7Ile | missense_variant | Exon 2 of 6 | 1 | NM_015722.4 | ENSP00000252939.4 | ||
ZNF511-PRAP1 | ENST00000368554.8 | c.506+17129C>A | intron_variant | Intron 4 of 7 | 2 | ENSP00000357542.5 | ||||
CALY | ENST00000368555.3 | c.20G>T | p.Ser7Ile | missense_variant | Exon 2 of 3 | 2 | ENSP00000357543.3 | |||
CALY | ENST00000368558.1 | c.20G>T | p.Ser7Ile | missense_variant | Exon 2 of 5 | 5 | ENSP00000357546.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.08e-7 AC: 1AN: 1412536Hom.: 0 Cov.: 31 AF XY: 0.00000143 AC XY: 1AN XY: 698118
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.20G>T (p.S7I) alteration is located in exon 2 (coding exon 1) of the CALY gene. This alteration results from a G to T substitution at nucleotide position 20, causing the serine (S) at amino acid position 7 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