chr16-20924009-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001128302.3(LYRM1):c.262C>T(p.Pro88Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000529 in 1,586,914 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001128302.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LYRM1 | NM_001128302.3 | c.262C>T | p.Pro88Ser | missense_variant | Exon 4 of 4 | ENST00000567954.6 | NP_001121774.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000784 AC: 19AN: 242430Hom.: 0 AF XY: 0.0000610 AC XY: 8AN XY: 131100
GnomAD4 exome AF: 0.0000537 AC: 77AN: 1434748Hom.: 0 Cov.: 27 AF XY: 0.0000489 AC XY: 35AN XY: 715126
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.262C>T (p.P88S) alteration is located in exon 5 (coding exon 3) of the LYRM1 gene. This alteration results from a C to T substitution at nucleotide position 262, causing the proline (P) at amino acid position 88 to be replaced by a serine (S). 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