rs2367202

Positions:

• chr2-86118413-A-G

Variant summary

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

The NM_017952.6(PTCD3):​c.415-508A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,106 control chromosomes in the GnomAD database, including 45,216 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 0.76 (45216 hom., cov: 32)
• Consequence: PTCD3 NM_017952.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

PTCD3 (HGNC:24717): (pentatricopeptide repeat domain 3) Enables rRNA binding activity and ribosomal small subunit binding activity. Involved in mitochondrial translation. Located in several cellular components, including cytosol; mitochondrion; and nucleoplasm. Implicated in combined oxidative phosphorylation deficiency 51. [provided by Alliance of Genome Resources, Apr 2022]

PTCD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCD3	NM_017952.6	c.415-508A>G		intron_variant		ENST00000254630.12	NP_060422.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCD3	ENST00000254630.12	c.415-508A>G		intron_variant		1	NM_017952.6	ENSP00000254630.7
PTCD3	ENST00000409783.6	c.414+1254A>G		intron_variant		5		ENSP00000386922.3
PTCD3	ENST00000465560.5	n.440-508A>G		intron_variant		3
PTCD3	ENST00000483925.1	n.316-508A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115626 AN: 151988 Hom.: 45192 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.761 AC: 115704 AN: 152106 Hom.: 45216 Cov.: 32 AF XY: 0.763 AC XY: 56714 AN XY: 74356

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.792

Alfa AF: 0.833 Hom.: 105502

Bravo AF: 0.752

Asia WGS AF: 0.736 AC: 2560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.051
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: rs2367202; hg19: chr2-86345536;