rs35678722
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024513.4(FYCO1):c.4265C>T(p.Thr1422Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000819 in 1,613,534 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024513.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FYCO1 | NM_024513.4 | c.4265C>T | p.Thr1422Met | missense_variant | 17/18 | ENST00000296137.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FYCO1 | ENST00000296137.7 | c.4265C>T | p.Thr1422Met | missense_variant | 17/18 | 1 | NM_024513.4 | P1 | |
FYCO1 | ENST00000433878.5 | c.632C>T | p.Thr211Met | missense_variant | 5/7 | 2 | |||
FYCO1 | ENST00000438446.1 | c.278C>T | p.Thr93Met | missense_variant | 5/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00363 AC: 553AN: 152142Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 264AN: 251460Hom.: 2 AF XY: 0.000706 AC XY: 96AN XY: 135900
GnomAD4 exome AF: 0.000524 AC: 766AN: 1461274Hom.: 3 Cov.: 31 AF XY: 0.000448 AC XY: 326AN XY: 727014
GnomAD4 genome ? AF: 0.00365 AC: 556AN: 152260Hom.: 4 Cov.: 32 AF XY: 0.00360 AC XY: 268AN XY: 74458
ClinVar
Submissions by phenotype
Cataract 18 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | FYCO1: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at