2-231732999-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002601.4(PDE6D):c.406G>A(p.Asp136Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000297 in 1,611,924 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. D136D) has been classified as Likely benign.
Frequency
Consequence
NM_002601.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE6D | NM_002601.4 | c.406G>A | p.Asp136Asn | missense_variant | Exon 5 of 5 | ENST00000287600.9 | NP_002592.1 | |
PDE6D | XM_047444726.1 | c.448G>A | p.Asp150Asn | missense_variant | Exon 5 of 5 | XP_047300682.1 | ||
PDE6D | NM_001291018.2 | c.*18G>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_001277947.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00165 AC: 251AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000393 AC: 98AN: 249078Hom.: 0 AF XY: 0.000230 AC XY: 31AN XY: 134818
GnomAD4 exome AF: 0.000156 AC: 228AN: 1459688Hom.: 2 Cov.: 28 AF XY: 0.000103 AC XY: 75AN XY: 726336
GnomAD4 genome AF: 0.00165 AC: 251AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00172 AC XY: 128AN XY: 74442
ClinVar
Submissions by phenotype
PDE6D-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Joubert syndrome 22 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at