rs1334893

Positions:

• chr10-27404376-G-A
• chr10-27404376-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

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]

ACMG classification

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
PTCHD3	NM_001034842.5	c.1212-1019C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCHD3	ENST00000642324.1	c.1212-1019C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143391 AN: 151986 Hom.: 67704 Cov.: 31

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

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

Other links and lift over

dbSNP: rs1334893; hg19: chr10-27693305;