chr11-123073748-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_024769.5(CLMP):c.848G>A(p.Arg283His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000253 in 1,604,368 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_024769.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLMP | NM_024769.5 | c.848G>A | p.Arg283His | missense_variant | 7/7 | ENST00000448775.4 | |
LOC124902775 | XR_007062927.1 | n.871-9266C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLMP | ENST00000448775.4 | c.848G>A | p.Arg283His | missense_variant | 7/7 | 1 | NM_024769.5 | P1 | |
ENST00000660892.2 | n.226+10235C>T | intron_variant, non_coding_transcript_variant | |||||||
CLMP | ENST00000527977.5 | n.670G>A | non_coding_transcript_exon_variant | 5/5 | 3 | ||||
CLMP | ENST00000530371.5 | n.322G>A | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000186 AC: 45AN: 242450Hom.: 0 AF XY: 0.000213 AC XY: 28AN XY: 131264
GnomAD4 exome AF: 0.000263 AC: 382AN: 1452062Hom.: 0 Cov.: 31 AF XY: 0.000235 AC XY: 170AN XY: 721894
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74480
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | The c.848G>A (p.R283H) alteration is located in exon 7 (coding exon 7) of the CLMP gene. This alteration results from a G to A substitution at nucleotide position 848, causing the arginine (R) at amino acid position 283 to be replaced by a histidine (H). 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