chr5-72359356-G-A

Position:

• chr5-72359356-G-A

Variant summary

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

The NM_024754.5(PTCD2):​c.*929G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,942 control chromosomes in the GnomAD database, including 5,440 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 0.26 (5440 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: PTCD2 NM_024754.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

PTCD2 (HGNC:25734): (pentatricopeptide repeat domain 2) Enables RNA binding activity. Predicted to be involved in mitochondrion organization and regulation of mRNA processing. Predicted to act upstream of or within animal organ development; muscle cell development; and regulation of gene expression. Located in mitochondrion. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCD2	NM_024754.5	c.*929G>A		3_prime_UTR_variant	10/10	ENST00000380639.10	NP_079030.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCD2	ENST00000380639.10	c.*929G>A		3_prime_UTR_variant	10/10	5	NM_024754.5	ENSP00000370013	P1
PTCD2	ENST00000308077.9	c.*397-248G>A		intron_variant, NMD_transcript_variant		1		ENSP00000308948
PTCD2	ENST00000536805.5			downstream_gene_variant		2		ENSP00000444772
PTCD2	ENST00000543322.5			downstream_gene_variant		2		ENSP00000438810

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39969 AN: 151824 Hom.: 5440 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.300

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.263 AC: 39986 AN: 151942 Hom.: 5440 Cov.: 31 AF XY: 0.260 AC XY: 19318 AN XY: 74232

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.302

Alfa AF: 0.259 Hom.: 676

Bravo AF: 0.273

Asia WGS AF: 0.319 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0080
DANN	Benign	0.37

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: rs2133729; hg19: chr5-71655183;