chr5-96727489-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001750.7(CAST):āc.337G>Cā(p.Ala113Pro) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000261 in 1,532,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001750.7 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
CAST | NM_001750.7 | c.337G>C | p.Ala113Pro | missense_variant, splice_region_variant | 6/32 | ENST00000675179.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAST | ENST00000675179.1 | c.337G>C | p.Ala113Pro | missense_variant, splice_region_variant | 6/32 | NM_001750.7 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151518Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000884 AC: 2AN: 226186Hom.: 0 AF XY: 0.00000814 AC XY: 1AN XY: 122908
GnomAD4 exome AF: 0.00000217 AC: 3AN: 1381132Hom.: 0 Cov.: 21 AF XY: 0.00000290 AC XY: 2AN XY: 689778
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151518Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73952
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.271G>C (p.A91P) alteration is located in exon 5 (coding exon 5) of the CAST gene. This alteration results from a G to C substitution at nucleotide position 271, causing the alanine (A) at amino acid position 91 to be replaced by a proline (P). 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