rs115701891
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_025009.5(CEP135):c.1675G>A(p.Ala559Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,597,440 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_025009.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP135 | NM_025009.5 | c.1675G>A | p.Ala559Thr | missense_variant | 13/26 | ENST00000257287.5 | NP_079285.2 | |
CEP135 | XM_006714055.4 | c.1642G>A | p.Ala548Thr | missense_variant | 13/26 | XP_006714118.1 | ||
CEP135 | XM_005265788.5 | c.604G>A | p.Ala202Thr | missense_variant | 6/19 | XP_005265845.1 | ||
CEP135 | XM_011534412.2 | c.145G>A | p.Ala49Thr | missense_variant | 3/16 | XP_011532714.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP135 | ENST00000257287.5 | c.1675G>A | p.Ala559Thr | missense_variant | 13/26 | 1 | NM_025009.5 | ENSP00000257287.3 | ||
CEP135 | ENST00000506202.1 | n.1625G>A | non_coding_transcript_exon_variant | 6/19 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0106 AC: 1605AN: 151972Hom.: 29 Cov.: 32
GnomAD3 exomes AF: 0.00269 AC: 634AN: 235322Hom.: 11 AF XY: 0.00198 AC XY: 252AN XY: 127456
GnomAD4 exome AF: 0.00102 AC: 1470AN: 1445350Hom.: 27 Cov.: 30 AF XY: 0.000892 AC XY: 641AN XY: 718268
GnomAD4 genome AF: 0.0106 AC: 1605AN: 152090Hom.: 29 Cov.: 32 AF XY: 0.0103 AC XY: 764AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 22, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 03, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at