chrX-23364549-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173495.3(PTCHD1):​c.352-15042G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 109,989 control chromosomes in the GnomAD database, including 3,622 homozygotes. There are 9,429 hemizygotes in GnomAD. 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 0.29 ( 3622 hom., 9429 hem., cov: 22)

Consequence

PTCHD1
NM_173495.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.913
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTCHD1NM_173495.3 linkuse as main transcriptc.352-15042G>C intron_variant ENST00000379361.5
PTCHD1XM_011545449.4 linkuse as main transcriptc.352-15042G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTCHD1ENST00000379361.5 linkuse as main transcriptc.352-15042G>C intron_variant 1 NM_173495.3 P1Q96NR3-1
PTCHD1ENST00000456522.1 linkuse as main transcriptc.159-27982G>C intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.289
AC:
31817
AN:
109940
Hom.:
3624
Cov.:
22
AF XY:
0.292
AC XY:
9406
AN XY:
32246
show subpopulations
Gnomad AFR
AF:
0.237
Gnomad AMI
AF:
0.187
Gnomad AMR
AF:
0.403
Gnomad ASJ
AF:
0.153
Gnomad EAS
AF:
0.574
Gnomad SAS
AF:
0.439
Gnomad FIN
AF:
0.339
Gnomad MID
AF:
0.355
Gnomad NFE
AF:
0.273
Gnomad OTH
AF:
0.326
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.289
AC:
31827
AN:
109989
Hom.:
3622
Cov.:
22
AF XY:
0.292
AC XY:
9429
AN XY:
32305
show subpopulations
Gnomad4 AFR
AF:
0.237
Gnomad4 AMR
AF:
0.404
Gnomad4 ASJ
AF:
0.153
Gnomad4 EAS
AF:
0.574
Gnomad4 SAS
AF:
0.440
Gnomad4 FIN
AF:
0.339
Gnomad4 NFE
AF:
0.273
Gnomad4 OTH
AF:
0.326
Alfa
AF:
0.137
Hom.:
657
Bravo
AF:
0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
16
DANN
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5971108; hg19: chrX-23382666; API