chr6-36823096-T-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_020939.2(CPNE5):c.98A>G(p.Asn33Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000702 in 1,566,942 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 1/1 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 missense, splice_region
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPNE5 | ENST00000244751.7 | c.98A>G | p.Asn33Ser | missense_variant, splice_region_variant | Exon 2 of 21 | 1 | NM_020939.2 | ENSP00000244751.2 | ||
CPNE5 | ENST00000633136.2 | c.98A>G | p.Asn33Ser | missense_variant, splice_region_variant | Exon 2 of 22 | 5 | ENSP00000487872.2 | |||
CPNE5 | ENST00000633280.1 | c.98A>G | p.Asn33Ser | missense_variant, splice_region_variant | Exon 2 of 10 | 5 | ENSP00000488125.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151954Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000174 AC: 4AN: 229914 AF XY: 0.00000804 show subpopulations
GnomAD4 exome AF: 0.0000742 AC: 105AN: 1414870Hom.: 1 Cov.: 30 AF XY: 0.0000713 AC XY: 50AN XY: 701674 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74372 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at