chr10-93612771-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006204.4(PDE6C):c.46A>C(p.Asn16His) variant causes a missense change. The variant allele was found at a frequency of 0.0000415 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N16K) has been classified as Uncertain significance.
Frequency
Consequence
NM_006204.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE6C | NM_006204.4 | c.46A>C | p.Asn16His | missense_variant | 1/22 | ENST00000371447.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE6C | ENST00000371447.4 | c.46A>C | p.Asn16His | missense_variant | 1/22 | 1 | NM_006204.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251494Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135922
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461844Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727212
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.46A>C (p.N16H) alteration is located in exon 1 (coding exon 1) of the PDE6C gene. This alteration results from a A to C substitution at nucleotide position 46, causing the asparagine (N) at amino acid position 16 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at