rs3210458
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001037172.3(PXYLP1):āc.1026C>Gā(p.Phe342Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000214 in 1,613,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001037172.3 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 |
---|---|---|---|---|---|---|---|
PXYLP1 | NM_001037172.3 | c.1026C>G | p.Phe342Leu | missense_variant | 6/6 | ENST00000286353.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXYLP1 | ENST00000286353.9 | c.1026C>G | p.Phe342Leu | missense_variant | 6/6 | 1 | NM_001037172.3 | P1 | |
ENST00000507698.1 | n.167-25180G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 250188Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 135180
GnomAD4 exome AF: 0.000216 AC: 315AN: 1460850Hom.: 0 Cov.: 31 AF XY: 0.000226 AC XY: 164AN XY: 726656
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74434
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at