X-23334893-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_173495.3(PTCHD1):c.18G>A(p.Leu6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000602 in 1,196,735 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 28 hemizygotes in GnomAD. 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. L6L) has been classified as Uncertain significance.
Frequency
Consequence
NM_173495.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCHD1 | NM_173495.3 | c.18G>A | p.Leu6= | synonymous_variant | 1/3 | ENST00000379361.5 | |
PTCHD1 | XM_011545449.4 | c.18G>A | p.Leu6= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD1 | ENST00000379361.5 | c.18G>A | p.Leu6= | synonymous_variant | 1/3 | 1 | NM_173495.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000909 AC: 1AN: 110007Hom.: 0 Cov.: 22 AF XY: 0.0000309 AC XY: 1AN XY: 32401
GnomAD3 exomes AF: 0.0000194 AC: 3AN: 154802Hom.: 0 AF XY: 0.0000203 AC XY: 1AN XY: 49190
GnomAD4 exome AF: 0.0000653 AC: 71AN: 1086728Hom.: 0 Cov.: 30 AF XY: 0.0000760 AC XY: 27AN XY: 355296
GnomAD4 genome ? AF: 0.00000909 AC: 1AN: 110007Hom.: 0 Cov.: 22 AF XY: 0.0000309 AC XY: 1AN XY: 32401
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 06, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at