rs1800857
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000730.3(CCKAR):c.113-5T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,611,920 control chromosomes in the GnomAD database, including 22,325 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000730.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCKAR | NM_000730.3 | c.113-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000295589.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCKAR | ENST00000295589.4 | c.113-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000730.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.177 AC: 26818AN: 151930Hom.: 2636 Cov.: 32
GnomAD3 exomes AF: 0.169 AC: 42004AN: 248440Hom.: 4163 AF XY: 0.176 AC XY: 23642AN XY: 134452
GnomAD4 exome AF: 0.153 AC: 223322AN: 1459872Hom.: 19687 Cov.: 34 AF XY: 0.158 AC XY: 114447AN XY: 726104
GnomAD4 genome ? AF: 0.177 AC: 26839AN: 152048Hom.: 2638 Cov.: 32 AF XY: 0.176 AC XY: 13106AN XY: 74322
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at