chr6-6654584-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004271.4(LY86):c.446G>C(p.Arg149Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. R149W) has been classified as Uncertain significance.
Frequency
Consequence
NM_004271.4 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 |
---|---|---|---|---|---|---|---|
LY86 | NM_004271.4 | c.446G>C | p.Arg149Pro | missense_variant | 5/5 | ENST00000230568.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LY86 | ENST00000230568.5 | c.446G>C | p.Arg149Pro | missense_variant | 5/5 | 1 | NM_004271.4 | P1 | |
LY86 | ENST00000379953.6 | c.446G>C | p.Arg149Pro | missense_variant | 6/6 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251314Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135818
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461832Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727214
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.446G>C (p.R149P) alteration is located in exon 5 (coding exon 5) of the LY86 gene. This alteration results from a G to C substitution at nucleotide position 446, causing the arginine (R) at amino acid position 149 to be replaced by a proline (P). 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