rs1675126
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001040694.2(INCENP):āc.1188T>Cā(p.Asn396=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 1,613,082 control chromosomes in the GnomAD database, including 639,712 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.88 ( 59570 hom., cov: 33)
Exomes š: 0.89 ( 580142 hom. )
Consequence
INCENP
NM_001040694.2 synonymous
NM_001040694.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.62
Genes affected
INCENP (HGNC:6058): (inner centromere protein) In mammalian cells, 2 broad groups of centromere-interacting proteins have been described: constitutively binding centromere proteins and 'passenger,' or transiently interacting, proteins (reviewed by Choo, 1997). The constitutive proteins include CENPA (centromere protein A; MIM 117139), CENPB (MIM 117140), CENPC1 (MIM 117141), and CENPD (MIM 117142). The term 'passenger proteins' encompasses a broad collection of proteins that localize to the centromere during specific stages of the cell cycle (Earnshaw and Mackay, 1994 [PubMed 8088460]). These include CENPE (MIM 117143); MCAK (MIM 604538); KID (MIM 603213); cytoplasmic dynein (e.g., MIM 600112); CliPs (e.g., MIM 179838); and CENPF/mitosin (MIM 600236). The inner centromere proteins (INCENPs) (Earnshaw and Cooke, 1991 [PubMed 1860899]), the initial members of the passenger protein group, display a broad localization along chromosomes in the early stages of mitosis but gradually become concentrated at centromeres as the cell cycle progresses into mid-metaphase. During telophase, the proteins are located within the midbody in the intercellular bridge, where they are discarded after cytokinesis (Cutts et al., 1999 [PubMed 10369859]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 11-62138902-T-C is Benign according to our data. Variant chr11-62138902-T-C is described in ClinVar as [Benign]. Clinvar id is 1261519.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.62 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INCENP | NM_001040694.2 | c.1188T>C | p.Asn396= | synonymous_variant | 7/19 | ENST00000394818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INCENP | ENST00000394818.8 | c.1188T>C | p.Asn396= | synonymous_variant | 7/19 | 1 | NM_001040694.2 | P2 | |
INCENP | ENST00000278849.4 | c.1188T>C | p.Asn396= | synonymous_variant | 7/18 | 5 | A2 | ||
INCENP | ENST00000528375.1 | n.157T>C | non_coding_transcript_exon_variant | 4/8 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.879 AC: 133634AN: 152082Hom.: 59517 Cov.: 33
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GnomAD3 exomes AF: 0.842 AC: 211370AN: 251046Hom.: 91209 AF XY: 0.839 AC XY: 113950AN XY: 135738
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GnomAD4 exome AF: 0.886 AC: 1294621AN: 1460880Hom.: 580142 Cov.: 39 AF XY: 0.882 AC XY: 641334AN XY: 726814
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GnomAD4 genome ? AF: 0.879 AC: 133746AN: 152202Hom.: 59570 Cov.: 33 AF XY: 0.866 AC XY: 64438AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
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