rs137853929
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_004750.5(CRLF1):c.31_53delCAATCCGCGCGGCGGCCGCCGCC(p.Gln11ValfsTer68) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,099,800 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_004750.5 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRLF1 | ENST00000392386.8 | c.31_53delCAATCCGCGCGGCGGCCGCCGCC | p.Gln11ValfsTer68 | frameshift_variant | Exon 1 of 9 | 1 | NM_004750.5 | ENSP00000376188.2 | ||
CRLF1 | ENST00000684169.1 | c.31_53delCAATCCGCGCGGCGGCCGCCGCC | p.Gln11ValfsTer68 | frameshift_variant | Exon 1 of 9 | ENSP00000506849.1 | ||||
CRLF1 | ENST00000593286.1 | n.367+749_367+771delCAATCCGCGCGGCGGCCGCCGCC | intron_variant | Intron 1 of 1 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000203 AC: 3AN: 147428Hom.: 0 Cov.: 29
GnomAD4 exome AF: 0.0000179 AC: 17AN: 952372Hom.: 0 AF XY: 0.0000313 AC XY: 14AN XY: 446584
GnomAD4 genome AF: 0.0000203 AC: 3AN: 147428Hom.: 0 Cov.: 29 AF XY: 0.0000139 AC XY: 1AN XY: 71832
ClinVar
Submissions by phenotype
Cold-induced sweating syndrome Pathogenic:1
Variant summary: CRLF1 c.31_53del23 (p.Gln11ValfsX68) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Variants downstream of this position have been classified as pathogenic in ClinVar. The variant was absent in 25332 control chromosomes (gnomAD). c.31_53del23 has been reported in the literature in a homozygous individual affected with Cold-Induced Sweating Syndrome (example: Yamazaki_2010). The following publication has been ascertained in the context of this evaluation (PMID: 20186812). One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Cold-induced sweating syndrome 1 Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at