chrX-23394819-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173495.3(PTCHD1):c.*634T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.60 ( 15356 hom., 19881 hem., cov: 24)
Exomes 𝑓: 0.44 ( 34 hom. 56 hem. )
Failed GnomAD Quality Control
Consequence
PTCHD1
NM_173495.3 3_prime_UTR
NM_173495.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0410
Publications
2 publications found
Genes affected
PTCHD1 (HGNC:26392): (patched domain containing 1) This gene encodes a membrane protein with a patched domain. The encoded protein is similar to Drosophila proteins which act as receptors for the morphogen sonic hedgehog. Deletions in this gene, which is located on the X chromosome, are associated with intellectual disability and autism (PMID: 21091464, PMID: 20844286). [provided by RefSeq, Aug 2011]
PTCHD1 Gene-Disease associations (from GenCC):
- autism, susceptibility to, X-linked 4Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), G2P
- non-syndromic X-linked intellectual disabilityInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.599 AC: 66756AN: 111379Hom.: 15359 Cov.: 24 show subpopulations
GnomAD3 genomes
AF:
AC:
66756
AN:
111379
Hom.:
Cov.:
24
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.437 AC: 212AN: 485Hom.: 34 Cov.: 0 AF XY: 0.397 AC XY: 56AN XY: 141 show subpopulations
GnomAD4 exome
AF:
AC:
212
AN:
485
Hom.:
Cov.:
0
AF XY:
AC XY:
56
AN XY:
141
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
5
AN:
23
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
AC:
4
AN:
8
European-Finnish (FIN)
AF:
AC:
131
AN:
280
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
69
AN:
165
Other (OTH)
AF:
AC:
3
AN:
9
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
4
9
13
18
22
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.600 AC: 66807AN: 111432Hom.: 15356 Cov.: 24 AF XY: 0.591 AC XY: 19881AN XY: 33620 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
66807
AN:
111432
Hom.:
Cov.:
24
AF XY:
AC XY:
19881
AN XY:
33620
show subpopulations
African (AFR)
AF:
AC:
26730
AN:
30667
American (AMR)
AF:
AC:
6023
AN:
10572
Ashkenazi Jewish (ASJ)
AF:
AC:
1527
AN:
2637
East Asian (EAS)
AF:
AC:
2227
AN:
3502
South Asian (SAS)
AF:
AC:
1226
AN:
2666
European-Finnish (FIN)
AF:
AC:
2651
AN:
5986
Middle Eastern (MID)
AF:
AC:
120
AN:
212
European-Non Finnish (NFE)
AF:
AC:
25135
AN:
52989
Other (OTH)
AF:
AC:
905
AN:
1524
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.509
Heterozygous variant carriers
0
886
1772
2658
3544
4430
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
580
1160
1740
2320
2900
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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