chr8-142785307-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003695.3(LY6D):c.301C>A(p.Pro101Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003695.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LY6D | NM_003695.3 | c.301C>A | p.Pro101Thr | missense_variant | 3/3 | ENST00000301263.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LY6D | ENST00000301263.5 | c.301C>A | p.Pro101Thr | missense_variant | 3/3 | 1 | NM_003695.3 | P1 | |
LY6D | ENST00000518434.1 | n.388C>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
LY6D | ENST00000518469.1 | n.998C>A | non_coding_transcript_exon_variant | 1/1 | |||||
LY6D | ENST00000518884.1 | n.494C>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249156Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135076
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461336Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 726992
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.301C>A (p.P101T) alteration is located in exon 3 (coding exon 3) of the LY6D gene. This alteration results from a C to A substitution at nucleotide position 301, causing the proline (P) at amino acid position 101 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