rs8058674
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014714.4(IFT140):c.838C>T(p.Arg280Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,613,818 control chromosomes in the GnomAD database, including 184 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R280Q) has been classified as Likely benign.
Frequency
Consequence
NM_014714.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.838C>T | p.Arg280Trp | missense_variant | 8/31 | ENST00000426508.7 | NP_055529.2 | |
LOC105371046 | NR_135176.1 | n.59+7412G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.838C>T | p.Arg280Trp | missense_variant | 8/31 | 5 | NM_014714.4 | ENSP00000406012 | P1 | |
ENST00000563162.1 | n.59+7412G>A | intron_variant, non_coding_transcript_variant | 2 | |||||||
IFT140 | ENST00000439987.6 | n.899C>T | non_coding_transcript_exon_variant | 7/19 | 2 | |||||
IFT140 | ENST00000397417.6 | c.329-3577C>T | intron_variant, NMD_transcript_variant | 5 | ENSP00000380562 |
Frequencies
GnomAD3 genomes AF: 0.0183 AC: 2790AN: 152156Hom.: 99 Cov.: 32
GnomAD3 exomes AF: 0.00479 AC: 1200AN: 250660Hom.: 40 AF XY: 0.00370 AC XY: 502AN XY: 135550
GnomAD4 exome AF: 0.00194 AC: 2833AN: 1461544Hom.: 84 Cov.: 30 AF XY: 0.00175 AC XY: 1272AN XY: 727066
GnomAD4 genome AF: 0.0184 AC: 2798AN: 152274Hom.: 100 Cov.: 32 AF XY: 0.0177 AC XY: 1316AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Saldino-Mainzer syndrome 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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at