rs778020037
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_014714.4(IFT140):c.1200C>T(p.Ser400=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000645 in 1,612,464 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000066 ( 1 hom. )
Consequence
IFT140
NM_014714.4 synonymous
NM_014714.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.76
Genes affected
IFT140 (HGNC:29077): (intraflagellar transport 140) This gene encodes one of the subunits of the intraflagellar transport (IFT) complex A. Intraflagellar transport is involved in the genesis, resorption and signaling of primary cilia. The primary cilium is a microtubule-based sensory organelle at the surface of most quiescent mammalian cells, that receives signals from its environment, such as the flow of fluid, light or odors, and transduces those signals to the nucleus. Loss of the corresponding protein in mouse results in renal cystic disease. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 16-1584376-G-A is Benign according to our data. Variant chr16-1584376-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 465314.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.76 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.1200C>T | p.Ser400= | synonymous_variant | 11/31 | ENST00000426508.7 | |
LOC105371046 | NR_135176.1 | n.59+3791G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.1200C>T | p.Ser400= | synonymous_variant | 11/31 | 5 | NM_014714.4 | P1 | |
ENST00000563162.1 | n.59+3791G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
IFT140 | ENST00000439987.6 | n.1261C>T | non_coding_transcript_exon_variant | 10/19 | 2 | ||||
IFT140 | ENST00000397417.6 | c.373C>T | p.Arg125Cys | missense_variant, NMD_transcript_variant | 4/24 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152160Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000125 AC: 31AN: 247272Hom.: 1 AF XY: 0.000127 AC XY: 17AN XY: 133814
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GnomAD4 exome AF: 0.0000664 AC: 97AN: 1460304Hom.: 1 Cov.: 31 AF XY: 0.0000592 AC XY: 43AN XY: 726360
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74330
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Saldino-Mainzer syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 20, 2023 | - - |
Retinal dystrophy Benign:1
Likely benign, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at