chr9-14842561-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_001379081.2(FREM1):c.1493G>A(p.Arg498Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000296 in 1,613,926 control chromosomes in the GnomAD database, including 2 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. R498W) has been classified as Likely benign.
Frequency
Consequence
NM_001379081.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FREM1 | NM_001379081.2 | c.1493G>A | p.Arg498Gln | missense_variant | 9/37 | ENST00000380880.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM1 | ENST00000380880.4 | c.1493G>A | p.Arg498Gln | missense_variant | 9/37 | 5 | NM_001379081.2 | P1 | |
FREM1 | ENST00000380875.7 | c.1493G>A | p.Arg498Gln | missense_variant, NMD_transcript_variant | 10/31 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000992 AC: 151AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000335 AC: 83AN: 247594Hom.: 1 AF XY: 0.000290 AC XY: 39AN XY: 134436
GnomAD4 exome AF: 0.000223 AC: 326AN: 1461652Hom.: 2 Cov.: 32 AF XY: 0.000205 AC XY: 149AN XY: 727112
GnomAD4 genome AF: 0.000992 AC: 151AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.00116 AC XY: 86AN XY: 74448
ClinVar
Submissions by phenotype
not provided Uncertain:3Benign:1Other:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 25, 2018 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Oculotrichoanal syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Trigonocephaly 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2011 | - - |
Rieger anomaly;C0344559:Irido-corneo-trabecular dysgenesis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Paul Sabatier University EA-4555, Paul Sabatier University | Jan 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at