12-42374867-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_201439.2(PPHLN1):āc.304A>Gā(p.Met102Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,450,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_201439.2 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 |
---|---|---|---|---|---|---|---|
PPHLN1 | NM_201439.2 | c.304A>G | p.Met102Val | missense_variant | 5/10 | ENST00000358314.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPHLN1 | ENST00000358314.12 | c.304A>G | p.Met102Val | missense_variant | 5/10 | 2 | NM_201439.2 | A1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 243752Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132382
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1450036Hom.: 0 Cov.: 32 AF XY: 0.00000554 AC XY: 4AN XY: 721804
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.304A>G (p.M102V) alteration is located in exon 5 (coding exon 4) of the PPHLN1 gene. This alteration results from a A to G substitution at nucleotide position 304, causing the methionine (M) at amino acid position 102 to be replaced by a valine (V). 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