chr3-9765903-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The ENST00000302036.12(OGG1):c.1043G>A(p.Gly348Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000695 in 1,613,956 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000302036.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMK1 | NM_003656.5 | c.84-13C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000256460.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMK1 | ENST00000256460.8 | c.84-13C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003656.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000540 AC: 82AN: 151962Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000441 AC: 111AN: 251452Hom.: 0 AF XY: 0.000515 AC XY: 70AN XY: 135910
GnomAD4 exome AF: 0.000711 AC: 1039AN: 1461876Hom.: 2 Cov.: 31 AF XY: 0.000683 AC XY: 497AN XY: 727244
GnomAD4 genome ? AF: 0.000539 AC: 82AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.000565 AC XY: 42AN XY: 74338
ClinVar
Submissions by phenotype
Nonpapillary renal cell carcinoma Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | May 10, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | Jan 22, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at