chrX-23364549-G-T

Variant names:

• chrX-23364549-G-T
• rs5971108
• NM_173495.3:c.352-15042G>T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_173495.3(PTCHD1):​c.352-15042G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000473 in 110,048 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 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 0.00047 (0 hom., 15 hem., cov: 22)
• Consequence: PTCHD1 NM_173495.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BS2: High Hemizygotes in GnomAd4 at 15 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD1	NM_173495.3	c.352-15042G>T		intron_variant	Intron 1 of 2	ENST00000379361.5	NP_775766.2
PTCHD1	XM_011545449.4	c.352-15042G>T		intron_variant	Intron 2 of 3		XP_011543751.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD1	ENST00000379361.5	c.352-15042G>T		intron_variant	Intron 1 of 2	1	NM_173495.3	ENSP00000368666.4
PTCHD1	ENST00000456522.1	c.157-27982G>T		intron_variant	Intron 1 of 1	1		ENSP00000406663.1

Frequencies

GnomAD3 genomes AF: 0.000482 AC: 53 AN: 109999 Hom.: 0 Cov.: 22 AF XY: 0.000434 AC XY: 14 AN XY: 32275

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000193

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000190

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.000473 AC: 52 AN: 110048 Hom.: 0 Cov.: 22 AF XY: 0.000464 AC XY: 15 AN XY: 32334

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000193

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0146

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000190

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.56

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

Other links and lift over

dbSNP: rs5971108; hg19: chrX-23382666;