16-89101226-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001243279.3(ACSF3):c.545C>T(p.Pro182Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,601,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P182P) has been classified as Likely benign.
Frequency
Consequence
NM_001243279.3 missense
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 |
---|---|---|---|---|---|---|---|
ACSF3 | NM_001243279.3 | c.545C>T | p.Pro182Leu | missense_variant | 3/11 | ENST00000614302.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSF3 | ENST00000614302.5 | c.545C>T | p.Pro182Leu | missense_variant | 3/11 | 5 | NM_001243279.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000180 AC: 40AN: 222772Hom.: 0 AF XY: 0.000174 AC XY: 21AN XY: 121034
GnomAD4 exome AF: 0.0000814 AC: 118AN: 1449258Hom.: 0 Cov.: 89 AF XY: 0.0000819 AC XY: 59AN XY: 720044
GnomAD4 genome AF: 0.000151 AC: 23AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74466
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 09, 2017 | - - |
Methylmalonic acidemia Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Combined malonic and methylmalonic acidemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at