rs121917816
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_014324.6(AMACR):āc.320T>Cā(p.Leu107Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000041 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L107M) has been classified as Uncertain significance.
Frequency
Consequence
NM_014324.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMACR | NM_014324.6 | c.320T>C | p.Leu107Pro | missense_variant | 2/5 | ENST00000335606.11 | |
C1QTNF3-AMACR | NR_037951.1 | n.837T>C | non_coding_transcript_exon_variant | 7/9 | |||
AMACR | NM_001167595.2 | c.320T>C | p.Leu107Pro | missense_variant | 2/6 | ||
AMACR | NM_203382.3 | c.320T>C | p.Leu107Pro | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMACR | ENST00000335606.11 | c.320T>C | p.Leu107Pro | missense_variant | 2/5 | 1 | NM_014324.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251420Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135896
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727242
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Congenital bile acid synthesis defect 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at