10-27399172-G-A
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001034842.5(PTCHD3):c.1426C>T(p.Arg476*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00683 in 1,607,094 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0044 ( 2 hom., cov: 30)
Exomes 𝑓: 0.0071 ( 64 hom. )
Consequence
PTCHD3
NM_001034842.5 stop_gained
NM_001034842.5 stop_gained
Scores
1
6
Clinical Significance
Conservation
PhyloP100: 0.765
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 10-27399172-G-A is Benign according to our data. Variant chr10-27399172-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640379.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27399172-G-A is described in Lovd as [Benign].
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTCHD3 | NM_001034842.5 | c.1426C>T | p.Arg476* | stop_gained | 4/4 | NP_001030014.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTCHD3 | ENST00000642324.1 | c.1426C>T | p.Arg476* | stop_gained | 4/4 | ENSP00000495205.1 |
Frequencies
GnomAD3 genomes AF: 0.00441 AC: 658AN: 149374Hom.: 2 Cov.: 30
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GnomAD3 exomes AF: 0.00522 AC: 1285AN: 246286Hom.: 10 AF XY: 0.00520 AC XY: 695AN XY: 133646
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GnomAD4 exome AF: 0.00708 AC: 10316AN: 1457624Hom.: 64 Cov.: 39 AF XY: 0.00679 AC XY: 4924AN XY: 725368
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GnomAD4 genome AF: 0.00440 AC: 657AN: 149470Hom.: 2 Cov.: 30 AF XY: 0.00388 AC XY: 282AN XY: 72642
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | PTCHD3: BS2 - |
Computational scores
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BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
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Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at