6-31710106-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001003693.3(LY6G6F):āc.727A>Gā(p.Met243Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,612,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001003693.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LY6G6F | NM_001003693.3 | c.727A>G | p.Met243Val | missense_variant | 4/6 | ENST00000375832.5 | NP_001003693.1 | |
LY6G6F-LY6G6D | NM_001353334.2 | c.727A>G | p.Met243Val | missense_variant | 4/6 | NP_001340263.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LY6G6F | ENST00000375832.5 | c.727A>G | p.Met243Val | missense_variant | 4/6 | 1 | NM_001003693.3 | ENSP00000364992.5 | ||
LY6G6F-LY6G6D | ENST00000503322.1 | c.727A>G | p.Met243Val | missense_variant | 4/6 | 1 | ENSP00000421232.1 | |||
ENSG00000204422 | ENST00000461287.1 | n.537+1911T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152094Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000406 AC: 10AN: 246456Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134346
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1460766Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 726702
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152094Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at