chr11-105026931-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001257118.3(CASP1):c.1027C>A(p.Pro343Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000308 in 1,593,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001257118.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASP1 | NM_001257118.3 | c.1027C>A | p.Pro343Thr | missense_variant | 8/9 | ENST00000533400.6 | |
LOC124902742 | XR_007062869.1 | n.41-4416G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASP1 | ENST00000533400.6 | c.1027C>A | p.Pro343Thr | missense_variant | 8/9 | 1 | NM_001257118.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000599 AC: 15AN: 250480Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135418
GnomAD4 exome AF: 0.0000146 AC: 21AN: 1440916Hom.: 0 Cov.: 27 AF XY: 0.0000125 AC XY: 9AN XY: 718244
GnomAD4 genome AF: 0.000184 AC: 28AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74410
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.1027C>A (p.P343T) alteration is located in exon 8 (coding exon 8) of the CASP1 gene. This alteration results from a C to A substitution at nucleotide position 1027, causing the proline (P) at amino acid position 343 to be replaced by a threonine (T). 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