rs1334893

Variant summary

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

The NM_001034842.5(PTCHD3):​c.1212-1019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 152,104 control chromosomes in the GnomAD database, including 67,762 homozygotes. 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 0.94 ( 67762 hom., cov: 31)

Consequence

PTCHD3
NM_001034842.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0870
Variant links:
Genes affected
PTCHD3 (HGNC:24776): (patched domain containing 3 (gene/pseudogene)) Predicted to be located in sperm midpiece. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTCHD3NM_001034842.5 linkuse as main transcriptc.1212-1019C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTCHD3ENST00000642324.1 linkuse as main transcriptc.1212-1019C>T intron_variant P1

Frequencies

GnomAD3 genomes
AF:
0.943
AC:
143391
AN:
151986
Hom.:
67704
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.958
Gnomad AMI
AF:
0.953
Gnomad AMR
AF:
0.957
Gnomad ASJ
AF:
0.944
Gnomad EAS
AF:
0.998
Gnomad SAS
AF:
0.956
Gnomad FIN
AF:
0.952
Gnomad MID
AF:
0.953
Gnomad NFE
AF:
0.925
Gnomad OTH
AF:
0.947
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.943
AC:
143508
AN:
152104
Hom.:
67762
Cov.:
31
AF XY:
0.947
AC XY:
70395
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.958
Gnomad4 AMR
AF:
0.957
Gnomad4 ASJ
AF:
0.944
Gnomad4 EAS
AF:
0.998
Gnomad4 SAS
AF:
0.955
Gnomad4 FIN
AF:
0.952
Gnomad4 NFE
AF:
0.925
Gnomad4 OTH
AF:
0.948
Alfa
AF:
0.932
Hom.:
117476
Bravo
AF:
0.945
Asia WGS
AF:
0.966
AC:
3354
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.2
DANN
Benign
0.49

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: rs1334893; hg19: chr10-27693305; API