Variant chr2-24790654-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001013663.2(PTRHD1):c.253-73C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 1,445,678 control chromosomes in the GnomAD database, including 177,082 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 15262 hom., cov: 32)

Exomes 𝑓: 0.50 ( 161820 hom. )

Consequence

PTRHD1
NM_001013663.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.899

Variant links:

Genes affected

PTRHD1 (HGNC:33782): (peptidyl-tRNA hydrolase domain containing 1) This gene encodes the enzyme peptidyl-tRNA hydrolase. Peptidyl-tRNA hydrolases perform the essential function of recycling peptidyl-tRNAs. Mutations in this gene are associated with autosomal-recessive intellectual disability and parkinsonism. [provided by RefSeq, May 2017]

PTRHD1 links:

LOC105369164 (HGNC:):

LOC105369164 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 2-24790654-G-C is Benign according to our data. Variant chr2-24790654-G-C is described in ClinVar as [Benign]. Clinvar id is 1221296.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
PTRHD1	NM_001013663.2 linkuse as main transcript	c.253-73C>G	intron_variant		ENST00000328379.6
LOC105369164	XR_939843.4 linkuse as main transcript	n.1636C>G	non_coding_transcript_exon_variant	3/3
LOC105369164	XR_001739341.2 linkuse as main transcript	n.868C>G	non_coding_transcript_exon_variant	4/4
LOC105369164	XR_007086245.1 linkuse as main transcript	n.1420C>G	non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTRHD1	ENST00000328379.6 linkuse as main transcript	c.253-73C>G		intron_variant		1	NM_001013663.2	P1

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63499

AN:

151910

Hom.:

15248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.576

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.562

Gnomad SAS

AF:

0.530

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.448

GnomAD4 exome

AF:

0.498

AC:

644335

AN:

1293650

Hom.:

161820

AF XY:

0.499

AC XY:

318305

AN XY:

638474

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.641

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.509

Gnomad4 SAS exome

AF:

0.516

Gnomad4 FIN exome

AF:

0.467

Gnomad4 NFE exome

AF:

0.504

Gnomad4 OTH exome

AF:

0.494

GnomAD4 genome

AF:

0.418

AC:

63508

AN:

152028

Hom.:

15262

Cov.:

AF XY:

0.422

AC XY:

31326

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.577

Gnomad4 ASJ

AF:

0.495

Gnomad4 EAS

AF:

0.562

Gnomad4 SAS

AF:

0.528

Gnomad4 FIN

AF:

0.458

Gnomad4 NFE

AF:

0.504

Gnomad4 OTH

AF:

0.454

Alfa

AF:

0.308

Hom.:

861

Bravo

AF:

0.415

Asia WGS

AF:

0.564

AC:

1958

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.31

DANN

Benign

0.38

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over