chr1-167433026-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP3
The NM_198053.3(CD247):c.427C>T(p.Gln143Ter) variant causes a stop gained, splice region change. The variant allele was found at a frequency of 0.00000821 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198053.3 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD247 | NM_198053.3 | c.427C>T | p.Gln143Ter | stop_gained, splice_region_variant | 7/8 | ENST00000362089.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD247 | ENST00000362089.10 | c.427C>T | p.Gln143Ter | stop_gained, splice_region_variant | 7/8 | 1 | NM_198053.3 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251262Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135840
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727218
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Immunodeficiency 25 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 20, 2020 | Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with CD247-related conditions. This variant is present in population databases (rs759213998, ExAC 0.02%). This sequence change creates a premature translational stop signal (p.Gln143*) in the CD247 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 22 amino acid(s) of the CD247 protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at