rs2133729

Variant names:

• chr5-72359356-G-A
• rs2133729
• NM_024754.5:c.*929G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTCD2	NM_024754.5	c.*929G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000380639.10	NP_079030.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCD2	ENST00000380639.10	c.*929G>A		3_prime_UTR_variant	Exon 10 of 10	5	NM_024754.5	ENSP00000370013.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.230 AC: 9524 AN: 41458

American (AMR) AF: 0.264 AC: 4029 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2195 AN: 5154

South Asian (SAS) AF: 0.267 AC: 1281 AN: 4792

European-Finnish (FIN) AF: 0.193 AC: 2034 AN: 10532

Middle Eastern (MID) AF: 0.407 AC: 118 AN: 290

European-Non Finnish (NFE) AF: 0.272 AC: 18478 AN: 67958

Other (OTH) AF: 0.302 AC: 638 AN: 2114

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
PhyloP100		-1.9
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: rs2133729; hg19: chr5-71655183;