chr16-1510942-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014714.4(IFT140):c.*2G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000505 in 1,610,274 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00044 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00051 ( 6 hom. )
Consequence
IFT140
NM_014714.4 3_prime_UTR
NM_014714.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0990
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 16-1510942-C-T is Benign according to our data. Variant chr16-1510942-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 281447.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00044 (67/152378) while in subpopulation SAS AF= 0.006 (29/4832). AF 95% confidence interval is 0.00429. There are 3 homozygotes in gnomad4. There are 43 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT140 | NM_014714.4 | c.*2G>A | 3_prime_UTR_variant | 31/31 | ENST00000426508.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT140 | ENST00000426508.7 | c.*2G>A | 3_prime_UTR_variant | 31/31 | 5 | NM_014714.4 | P1 | ||
IFT140 | ENST00000361339.9 | c.*2G>A | 3_prime_UTR_variant | 13/13 | 1 | ||||
IFT140 | ENST00000565298.5 | n.4215G>A | non_coding_transcript_exon_variant | 19/19 | 2 | ||||
IFT140 | ENST00000397417.6 | c.*2829G>A | 3_prime_UTR_variant, NMD_transcript_variant | 24/24 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000433 AC: 66AN: 152260Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.000727 AC: 178AN: 244692Hom.: 3 AF XY: 0.000919 AC XY: 122AN XY: 132740
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GnomAD4 exome AF: 0.000512 AC: 746AN: 1457896Hom.: 6 Cov.: 32 AF XY: 0.000668 AC XY: 484AN XY: 724974
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GnomAD4 genome ? AF: 0.000440 AC: 67AN: 152378Hom.: 3 Cov.: 33 AF XY: 0.000577 AC XY: 43AN XY: 74516
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 18, 2015 | - - |
Saldino-Mainzer syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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