11-126269044-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000532125(FOXRED1):c.-163G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00069 in 746,570 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000532125 5_prime_UTR
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 rank | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXRED1 | ENST00000692336 | c.-163G>C | 5_prime_UTR_variant | Exon 1 of 11 | ENSP00000508540.1 | |||||
FOXRED1 | ENST00000532125 | c.-163G>C | 5_prime_UTR_variant | Exon 1 of 11 | 2 | ENSP00000434178.2 | ||||
FOXRED1 | ENST00000685484 | c.-163G>C | 5_prime_UTR_variant | Exon 1 of 10 | ENSP00000510622.1 |
Frequencies
GnomAD3 genomes AF: 0.00234 AC: 356AN: 152274Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000503 AC: 63AN: 125152Hom.: 0 AF XY: 0.000357 AC XY: 24AN XY: 67308
GnomAD4 exome AF: 0.000269 AC: 160AN: 594178Hom.: 0 Cov.: 7 AF XY: 0.000202 AC XY: 64AN XY: 317510
GnomAD4 genome AF: 0.00233 AC: 355AN: 152392Hom.: 3 Cov.: 33 AF XY: 0.00221 AC XY: 165AN XY: 74518
ClinVar
Submissions by phenotype
Mitochondrial complex I deficiency, nuclear type 1 Uncertain:1
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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at