17-27882676-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001076680.3(LYRM9):c.19G>A(p.Ala7Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000344 in 1,452,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A7V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001076680.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LYRM9 | ENST00000379102.8 | c.19G>A | p.Ala7Thr | missense_variant | Exon 2 of 4 | 2 | NM_001076680.3 | ENSP00000368396.3 | ||
ENSG00000266202 | ENST00000582441.1 | c.19G>A | p.Ala7Thr | missense_variant | Exon 2 of 5 | 4 | ENSP00000462879.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000215 AC: 5AN: 232890Hom.: 0 AF XY: 0.0000238 AC XY: 3AN XY: 126048
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1452036Hom.: 0 Cov.: 30 AF XY: 0.00000416 AC XY: 3AN XY: 721212
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.19G>A (p.A7T) alteration is located in exon 2 (coding exon 1) of the LYRM9 gene. This alteration results from a G to A substitution at nucleotide position 19, causing the alanine (A) at amino acid position 7 to be replaced by a threonine (T). 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