chr16-1510954-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014714.4(IFT140):āc.4379A>Gā(p.Asp1460Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,611,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_014714.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.4379A>G | p.Asp1460Gly | missense_variant | 31/31 | ENST00000426508.7 | NP_055529.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.4379A>G | p.Asp1460Gly | missense_variant | 31/31 | 5 | NM_014714.4 | ENSP00000406012 | P1 | |
IFT140 | ENST00000361339.9 | c.1961A>G | p.Asp654Gly | missense_variant | 13/13 | 1 | ENSP00000354895 | |||
IFT140 | ENST00000565298.5 | n.4203A>G | non_coding_transcript_exon_variant | 19/19 | 2 | |||||
IFT140 | ENST00000397417.6 | c.*2817A>G | 3_prime_UTR_variant, NMD_transcript_variant | 24/24 | 5 | ENSP00000380562 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000812 AC: 2AN: 246298Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133582
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459278Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 725724
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74380
ClinVar
Submissions by phenotype
Saldino-Mainzer syndrome;C4540439:Retinitis pigmentosa 80 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 18, 2021 | - - |
Saldino-Mainzer syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 13, 2021 | Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with IFT140-related conditions. This variant is present in population databases (rs771632573, gnomAD 0.01%). This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 1460 of the IFT140 protein (p.Asp1460Gly). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at