rs759442715
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_018288.4(PHF10):c.1385G>T(p.Cys462Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_018288.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF10 | NM_018288.4 | c.1385G>T | p.Cys462Phe | missense_variant | Exon 11 of 12 | ENST00000339209.9 | NP_060758.2 | |
C6orf120 | NM_001029863.3 | c.*2124C>A | 3_prime_UTR_variant | Exon 1 of 1 | ENST00000332290.4 | NP_001025034.1 | ||
PHF10 | NM_133325.3 | c.1379G>T | p.Cys460Phe | missense_variant | Exon 11 of 12 | NP_579866.2 | ||
C6orf120 | NM_001317342.2 | c.*2124C>A | 3_prime_UTR_variant | Exon 2 of 2 | NP_001304271.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHF10 | ENST00000339209.9 | c.1385G>T | p.Cys462Phe | missense_variant | Exon 11 of 12 | 1 | NM_018288.4 | ENSP00000341805.4 | ||
PHF10 | ENST00000621772.4 | c.1244G>T | p.Cys415Phe | missense_variant | Exon 11 of 12 | 1 | ENSP00000484117.1 | |||
C6orf120 | ENST00000332290.4 | c.*2124C>A | 3_prime_UTR_variant | Exon 1 of 1 | 6 | NM_001029863.3 | ENSP00000346931.1 | |||
PHF10 | ENST00000366780.8 | c.1379G>T | p.Cys460Phe | missense_variant | Exon 11 of 12 | 5 | ENSP00000355743.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247056Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133524
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457916Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725042
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at