rs2242653
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001003693.3(LY6G6F):c.500G>A(p.Arg167Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,612,924 control chromosomes in the GnomAD database, including 20,791 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001003693.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LY6G6F | NM_001003693.3 | c.500G>A | p.Arg167Lys | missense_variant | 3/6 | ENST00000375832.5 | |
LY6G6F-LY6G6D | NM_001353334.2 | c.500G>A | p.Arg167Lys | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LY6G6F | ENST00000375832.5 | c.500G>A | p.Arg167Lys | missense_variant | 3/6 | 1 | NM_001003693.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.153 AC: 23193AN: 152056Hom.: 2068 Cov.: 32
GnomAD3 exomes AF: 0.169 AC: 41685AN: 246648Hom.: 4177 AF XY: 0.164 AC XY: 22031AN XY: 134408
GnomAD4 exome AF: 0.152 AC: 222593AN: 1460750Hom.: 18718 Cov.: 35 AF XY: 0.151 AC XY: 109734AN XY: 726686
GnomAD4 genome ? AF: 0.153 AC: 23219AN: 152174Hom.: 2073 Cov.: 32 AF XY: 0.161 AC XY: 11949AN XY: 74378
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at