rs587776965
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_024769.5(CLMP):c.821G>A(p.Arg274Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000186 in 1,613,632 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 Pathogenic (no stars).
Frequency
Consequence
NM_024769.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLMP | ENST00000448775.4 | c.821G>A | p.Arg274Gln | missense_variant, splice_region_variant | Exon 6 of 7 | 1 | NM_024769.5 | ENSP00000405577.2 | ||
CLMP | ENST00000527977.5 | n.643G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 4 of 5 | 3 | |||||
CLMP | ENST00000530371.5 | n.295G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 3 of 4 | 4 | |||||
ENSG00000288061 | ENST00000660892.2 | n.227-9671C>T | intron_variant | Intron 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152014Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251192Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135774
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461618Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727116
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152014Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74264
ClinVar
Submissions by phenotype
Congenital short bowel syndrome, autosomal recessive Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at