chr6-6649672-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004271.4(LY86):c.400C>T(p.Pro134Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000493 in 1,561,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004271.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000257 AC: 39AN: 152014Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000691 AC: 17AN: 246078Hom.: 0 AF XY: 0.0000451 AC XY: 6AN XY: 133066
GnomAD4 exome AF: 0.0000270 AC: 38AN: 1409230Hom.: 0 Cov.: 24 AF XY: 0.0000213 AC XY: 15AN XY: 704114
GnomAD4 genome AF: 0.000256 AC: 39AN: 152132Hom.: 0 Cov.: 34 AF XY: 0.000269 AC XY: 20AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.400C>T (p.P134S) alteration is located in exon 4 (coding exon 4) of the LY86 gene. This alteration results from a C to T substitution at nucleotide position 400, causing the proline (P) at amino acid position 134 to be replaced by a serine (S). 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