X-101127186-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001386188.2(CENPI):c.826G>A(p.Val276Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000997 in 1,189,898 control chromosomes in the GnomAD database, including 6 homozygotes. There are 342 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPI | NM_001386188.2 | c.826G>A | p.Val276Met | missense_variant | 10/22 | ENST00000682095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPI | ENST00000682095.1 | c.826G>A | p.Val276Met | missense_variant | 10/22 | NM_001386188.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00497 AC: 555AN: 111759Hom.: 4 Cov.: 23 AF XY: 0.00471 AC XY: 160AN XY: 33971
GnomAD3 exomes AF: 0.00153 AC: 265AN: 172702Hom.: 3 AF XY: 0.00106 AC XY: 62AN XY: 58434
GnomAD4 exome AF: 0.000584 AC: 630AN: 1078086Hom.: 2 Cov.: 28 AF XY: 0.000520 AC XY: 181AN XY: 347744
GnomAD4 genome AF: 0.00497 AC: 556AN: 111812Hom.: 4 Cov.: 23 AF XY: 0.00473 AC XY: 161AN XY: 34034
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at