chr8-142703201-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017527.4(LY6K):āc.328T>Cā(p.Phe110Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000942 in 1,614,238 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017527.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LY6K | NM_017527.4 | c.328T>C | p.Phe110Leu | missense_variant | 3/3 | ENST00000292430.10 | |
LNCOC1 | NR_038925.1 | n.4735A>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LY6K | ENST00000292430.10 | c.328T>C | p.Phe110Leu | missense_variant | 3/3 | 1 | NM_017527.4 | P2 | |
LNCOC1 | ENST00000669349.1 | n.2850A>G | non_coding_transcript_exon_variant | 6/6 |
Frequencies
GnomAD3 genomes AF: 0.000434 AC: 66AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251492Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135922
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.0000523 AC XY: 38AN XY: 727246
GnomAD4 genome AF: 0.000466 AC: 71AN: 152346Hom.: 1 Cov.: 33 AF XY: 0.000523 AC XY: 39AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.328T>C (p.F110L) alteration is located in exon 3 (coding exon 3) of the LY6K gene. This alteration results from a T to C substitution at nucleotide position 328, causing the phenylalanine (F) at amino acid position 110 to be replaced by a leucine (L). 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