chr11-117361836-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014956.5(CEP164):āc.395C>Gā(p.Ala132Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,614,200 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A132S) has been classified as Uncertain significance.
Frequency
Consequence
NM_014956.5 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
CEP164 | NM_014956.5 | c.395C>G | p.Ala132Gly | missense_variant, splice_region_variant | 6/33 | ENST00000278935.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP164 | ENST00000278935.8 | c.395C>G | p.Ala132Gly | missense_variant, splice_region_variant | 6/33 | 1 | NM_014956.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00577 AC: 878AN: 152214Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00150 AC: 377AN: 251442Hom.: 4 AF XY: 0.00111 AC XY: 151AN XY: 135900
GnomAD4 exome AF: 0.000605 AC: 884AN: 1461868Hom.: 7 Cov.: 31 AF XY: 0.000516 AC XY: 375AN XY: 727236
GnomAD4 genome AF: 0.00578 AC: 880AN: 152332Hom.: 11 Cov.: 32 AF XY: 0.00587 AC XY: 437AN XY: 74482
ClinVar
Submissions by phenotype
Nephronophthisis 15 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at