Variant chr13-24421321-T-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006437.4(PARP4):c.4980-8_4980-7insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 2116 hom., cov: 0)

Exomes 𝑓: 0.10 ( 115 hom. )

Failed GnomAD Quality Control

Consequence

PARP4
NM_006437.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.76

Variant links:

Genes affected

PARP4 (HGNC:271): (poly(ADP-ribose) polymerase family member 4) This gene encodes poly(ADP-ribosyl)transferase-like 1 protein, which is capable of catalyzing a poly(ADP-ribosyl)ation reaction. This protein has a catalytic domain which is homologous to that of poly (ADP-ribosyl) transferase, but lacks an N-terminal DNA binding domain which activates the C-terminal catalytic domain of poly (ADP-ribosyl) transferase. Since this protein is not capable of binding DNA directly, its transferase activity may be activated by other factors such as protein-protein interaction mediated by the extensive carboxyl terminus. [provided by RefSeq, Jul 2008]

PARP4 links:

TPTE2P6 (HGNC:42644): (TPTE2 pseudogene 6)

TPTE2P6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 13-24421321-T-TA is Benign according to our data. Variant chr13-24421321-T-TA is described in ClinVar as [Benign]. Clinvar id is 2796426.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARP4	NM_006437.4 linkuse as main transcript	c.4980-8_4980-7insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000381989.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARP4	ENST00000381989.4 linkuse as main transcript	c.4980-8_4980-7insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_006437.4	P1
TPTE2P6	ENST00000445572.5 linkuse as main transcript	n.233+12027dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

24523

AN:

111128

Hom.:

2119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.295

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.205

GnomAD3 exomes

AF:

0.0000713

AC:

AN:

14024

Hom.:

AF XY:

0.00

AC XY:

AN XY:

7106

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000199

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.101

AC:

95807

AN:

952748

Hom.:

115

Cov.:

AF XY:

0.102

AC XY:

47696

AN XY:

468880

show subpopulations

Gnomad4 AFR exome

AF:

0.0880

Gnomad4 AMR exome

AF:

0.132

Gnomad4 ASJ exome

AF:

0.158

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.0653

Gnomad4 FIN exome

AF:

0.154

Gnomad4 NFE exome

AF:

0.0954

Gnomad4 OTH exome

AF:

0.122

GnomAD4 genome

AF:

0.220

AC:

24506

AN:

111192

Hom.:

2116

Cov.:

AF XY:

0.209

AC XY:

11140

AN XY:

53198

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.204

Gnomad4 ASJ

AF:

0.275

Gnomad4 EAS

AF:

0.261

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.208

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 17, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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