10-27399255-AAAAAG-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001034842.5(PTCHD3):c.1358-20_1358-16del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,173,578 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: PTCHD3 NM_001034842.5 splice_polypyrimidine_tract, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.88

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 10-27399255-AAAAAG-A is Benign according to our data. Variant chr10-27399255-AAAAAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2798121.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCHD3	NM_001034842.5	c.1358-20_1358-16del		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCHD3	ENST00000642324.1	c.1358-20_1358-16del		splice_polypyrimidine_tract_variant, intron_variant				P1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 0.000112 AC: 131 AN: 1173578 Hom.: 0 AF XY: 0.000105 AC XY: 62 AN XY: 587924

Gnomad4 AFR exome AF: 0.000184

Gnomad4 AMR exome AF: 0.0000663

Gnomad4 ASJ exome AF: 0.0000494

Gnomad4 EAS exome AF: 0.0000262

Gnomad4 SAS exome AF: 0.000134

Gnomad4 FIN exome AF: 0.000143

Gnomad4 NFE exome AF: 0.000113

Gnomad4 OTH exome AF: 0.000120

GnomAD4 genome Cov.: 24

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 30, 2023

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750787130; hg19: chr10-27688184;