chr11-123084547-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.353G>A(p.Arg118His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.353G>A | p.Arg118His | missense_variant | 3/7 | ENST00000448775.4 | |
LOC124902775 | XR_007062927.1 | n.2404C>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLMP | ENST00000448775.4 | c.353G>A | p.Arg118His | missense_variant | 3/7 | 1 | NM_024769.5 | P1 | |
ENST00000660892.2 | n.401C>T | non_coding_transcript_exon_variant | 3/3 | ||||||
CLMP | ENST00000527977.5 | n.168G>A | non_coding_transcript_exon_variant | 1/5 | 3 | ||||
CLMP | ENST00000529128.1 | n.339G>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251288Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135848
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727232
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.353G>A (p.R118H) alteration is located in exon 3 (coding exon 3) of the CLMP gene. This alteration results from a G to A substitution at nucleotide position 353, causing the arginine (R) at amino acid position 118 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