rs3752480
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020939.2(CPNE5):c.1564-6T>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 0.194 in 1,607,348 control chromosomes in the GnomAD database, including 31,702 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 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_020939.2 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 |
---|---|---|---|---|---|---|---|
CPNE5 | NM_020939.2 | c.1564-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000244751.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPNE5 | ENST00000244751.7 | c.1564-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020939.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25211AN: 151938Hom.: 2398 Cov.: 32
GnomAD3 exomes AF: 0.195 AC: 48092AN: 246112Hom.: 4956 AF XY: 0.198 AC XY: 26394AN XY: 133358
GnomAD4 exome AF: 0.197 AC: 286647AN: 1455292Hom.: 29307 Cov.: 35 AF XY: 0.198 AC XY: 143503AN XY: 723504
GnomAD4 genome ? AF: 0.166 AC: 25195AN: 152056Hom.: 2395 Cov.: 32 AF XY: 0.167 AC XY: 12425AN XY: 74338
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at