13-49506711-A-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001040443.3(PHF11):āc.171A>Cā(p.Leu57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000046 in 1,607,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L57L) has been classified as Benign.
Frequency
Consequence
NM_001040443.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF11 | NM_001040443.3 | c.171A>C | p.Leu57= | synonymous_variant | 2/10 | ENST00000378319.8 | |
SETDB2-PHF11 | NR_135324.2 | n.2663-6348A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF11 | ENST00000378319.8 | c.171A>C | p.Leu57= | synonymous_variant | 2/10 | 1 | NM_001040443.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151860Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 250890Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135636
GnomAD4 exome AF: 0.0000474 AC: 69AN: 1455828Hom.: 0 Cov.: 30 AF XY: 0.0000745 AC XY: 54AN XY: 724742
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151860Hom.: 0 Cov.: 30 AF XY: 0.0000674 AC XY: 5AN XY: 74168
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at