rs201092215
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_152424.4(AMER1):c.2651C>T(p.Pro884Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000711 in 1,210,356 control chromosomes in the GnomAD database, including 6 homozygotes. There are 280 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_152424.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMER1 | NM_152424.4 | c.2651C>T | p.Pro884Leu | missense_variant | 2/2 | ENST00000374869.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMER1 | ENST00000374869.8 | c.2651C>T | p.Pro884Leu | missense_variant | 2/2 | 5 | NM_152424.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00158 AC: 177AN: 112105Hom.: 2 Cov.: 23 AF XY: 0.00140 AC XY: 48AN XY: 34259
GnomAD3 exomes AF: 0.00108 AC: 195AN: 181237Hom.: 3 AF XY: 0.000909 AC XY: 61AN XY: 67133
GnomAD4 exome AF: 0.000622 AC: 683AN: 1098197Hom.: 4 Cov.: 35 AF XY: 0.000638 AC XY: 232AN XY: 363553
GnomAD4 genome AF: 0.00158 AC: 177AN: 112159Hom.: 2 Cov.: 23 AF XY: 0.00140 AC XY: 48AN XY: 34323
ClinVar
Submissions by phenotype
not provided Benign:6
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 13, 2016 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at