rs143507892
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000290866.10(ACE):c.2858G>A(p.Arg953Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000572 in 1,614,166 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R953W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000290866.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACE | NM_000789.4 | c.2858G>A | p.Arg953Gln | missense_variant | 19/25 | ENST00000290866.10 | NP_000780.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACE | ENST00000290866.10 | c.2858G>A | p.Arg953Gln | missense_variant | 19/25 | 1 | NM_000789.4 | ENSP00000290866 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 282AN: 251298Hom.: 2 AF XY: 0.00157 AC XY: 213AN XY: 135858
GnomAD4 exome AF: 0.000603 AC: 882AN: 1461864Hom.: 11 Cov.: 31 AF XY: 0.000831 AC XY: 604AN XY: 727242
GnomAD4 genome AF: 0.000269 AC: 41AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74466
ClinVar
Submissions by phenotype
Renal tubular dysgenesis Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Jan 01, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at