chr10-27404376-G-A

Variant names:

• chr10-27404376-G-A
• rs1334893
• ENST00000642324.1:c.1212-1019C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642324.1(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 ENST00000642324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 9 publications found

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]

ENSG00000301548 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642324.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD3	NM_001034842.5		c.1212-1019C>T		intron	N/A	NP_001030014.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD3	ENST00000642324.1		c.1212-1019C>T		intron	N/A	ENSP00000495205.1
	ENSG00000301548	ENST00000779634.1		n.85+32673G>A		intron	N/A
	ENSG00000301548	ENST00000779635.1		n.86-13841G>A		intron	N/A

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

African (AFR) AF: 0.958 AC: 39753 AN: 41508

American (AMR) AF: 0.957 AC: 14607 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3276 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5178 AN: 5190

South Asian (SAS) AF: 0.955 AC: 4597 AN: 4812

European-Finnish (FIN) AF: 0.952 AC: 10057 AN: 10568

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62889 AN: 67984

Other (OTH) AF: 0.948 AC: 2000 AN: 2110

Alfa AF: 0.933 Hom.: 184561

Bravo AF: 0.945

Asia WGS AF: 0.966 AC: 3354 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		0.087
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1334893; hg19: chr10-27693305;