X-101101098-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001386188.2(CENPI):c.28G>A(p.Val10Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000191 in 1,208,831 control chromosomes in the GnomAD database, including 1 homozygotes. There are 72 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001386188.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPI | NM_001386188.2 | c.28G>A | p.Val10Ile | missense_variant | 3/22 | ENST00000682095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPI | ENST00000682095.1 | c.28G>A | p.Val10Ile | missense_variant | 3/22 | NM_001386188.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 25AN: 111947Hom.: 0 Cov.: 24 AF XY: 0.000323 AC XY: 11AN XY: 34101
GnomAD3 exomes AF: 0.000551 AC: 101AN: 183235Hom.: 0 AF XY: 0.000340 AC XY: 23AN XY: 67727
GnomAD4 exome AF: 0.000188 AC: 206AN: 1096834Hom.: 1 Cov.: 30 AF XY: 0.000168 AC XY: 61AN XY: 362240
GnomAD4 genome ? AF: 0.000223 AC: 25AN: 111997Hom.: 0 Cov.: 24 AF XY: 0.000322 AC XY: 11AN XY: 34163
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at