chr6-31720150-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025261.3(LY6G6C):c.106C>T(p.Arg36Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,612,946 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. R36Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_025261.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LY6G6C | NM_025261.3 | c.106C>T | p.Arg36Trp | missense_variant | 2/3 | ENST00000375819.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LY6G6C | ENST00000375819.3 | c.106C>T | p.Arg36Trp | missense_variant | 2/3 | 1 | NM_025261.3 | P1 | |
LY6G6C | ENST00000495859.1 | c.-63C>T | 5_prime_UTR_variant | 3/4 | 1 | ||||
MPIG6B | ENST00000460663.5 | n.90+1467G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246724Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134390
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1460750Hom.: 0 Cov.: 31 AF XY: 0.0000317 AC XY: 23AN XY: 726694
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.106C>T (p.R36W) alteration is located in exon 2 (coding exon 2) of the LY6G6C gene. This alteration results from a C to T substitution at nucleotide position 106, causing the arginine (R) at amino acid position 36 to be replaced by a tryptophan (W). 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