chr9-93645671-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_005392.4(PHF2):c.342G>A(p.Thr114Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 1,611,392 control chromosomes in the GnomAD database, including 345 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_005392.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHF2 | ENST00000359246.9 | c.342G>A | p.Thr114Thr | synonymous_variant | Exon 4 of 22 | 1 | NM_005392.4 | ENSP00000352185.4 | ||
PHF2 | ENST00000610682.1 | c.239+9206G>A | intron_variant | Intron 3 of 7 | 5 | ENSP00000479936.1 | ||||
PHF2 | ENST00000375376.8 | c.187-7596G>A | intron_variant | Intron 3 of 8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0210 AC: 3197AN: 152224Hom.: 44 Cov.: 34
GnomAD3 exomes AF: 0.0188 AC: 4706AN: 249840Hom.: 68 AF XY: 0.0192 AC XY: 2596AN XY: 135042
GnomAD4 exome AF: 0.0180 AC: 26284AN: 1459050Hom.: 301 Cov.: 32 AF XY: 0.0182 AC XY: 13188AN XY: 725638
GnomAD4 genome AF: 0.0210 AC: 3199AN: 152342Hom.: 44 Cov.: 34 AF XY: 0.0224 AC XY: 1669AN XY: 74484
ClinVar
Submissions by phenotype
PHF2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at