chr2-86138484-T-C

Position:

• chr2-86138484-T-C

Variant summary

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

The NM_017952.6(PTCD3):​c.*925T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,088 control chromosomes in the GnomAD database, including 12,900 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 0.37 (12897 hom., cov: 31)
  • Exomes 𝑓: 0.43 (3 hom.)
• Consequence: PTCD3 NM_017952.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCD3	NM_017952.6	c.*925T>C		3_prime_UTR_variant	24/24	ENST00000254630.12	NP_060422.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCD3	ENST00000254630.12	c.*925T>C		3_prime_UTR_variant	24/24	1	NM_017952.6	ENSP00000254630.7

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56391 AN: 151942 Hom.: 12902 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.429 AC: 12 AN: 28 Hom.: 3 Cov.: 0 AF XY: 0.417 AC XY: 10 AN XY: 24

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.389

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.371 AC: 56372 AN: 152060 Hom.: 12897 Cov.: 31 AF XY: 0.369 AC XY: 27404 AN XY: 74292

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.394

Alfa AF: 0.471 Hom.: 24302

Bravo AF: 0.351

Asia WGS AF: 0.264 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.57

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: rs11395; hg19: chr2-86365607;