Variant chr7-98881057-A-G 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_001375524.1(TRRAP):c.-61-33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 1,019,080 control chromosomes in the GnomAD database, including 7,400 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 4280 hom., cov: 31)

Exomes 𝑓: 0.053 ( 3120 hom. )

Consequence

TRRAP
NM_001375524.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0740

Variant links:

Genes affected

TRRAP (HGNC:12347): (transformation/transcription domain associated protein) This gene encodes a large multidomain protein of the phosphoinositide 3-kinase-related kinases (PIKK) family. The encoded protein is a common component of many histone acetyltransferase (HAT) complexes and plays a role in transcription and DNA repair by recruiting HAT complexes to chromatin. Deregulation of this gene may play a role in several types of cancer including glioblastoma multiforme. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]

TRRAP 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=-0.9).

BP6

Variant 7-98881057-A-G is Benign according to our data. Variant chr7-98881057-A-G is described in ClinVar as [Benign]. Clinvar id is 1222828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
TRRAP	NM_001375524.1 linkuse as main transcript	c.-61-33A>G	intron_variant	ENST00000456197.2
TRRAP	NM_001244580.2 linkuse as main transcript	c.-61-33A>G	intron_variant
TRRAP	NM_003496.4 linkuse as main transcript	c.-61-33A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRRAP	ENST00000456197.2 linkuse as main transcript	c.-61-33A>G		intron_variant		1	NM_001375524.1	P2

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23633

AN:

152066

Hom.:

4255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0815

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0574

Gnomad FIN

AF:

0.0232

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0416

Gnomad OTH

AF:

0.135

GnomAD4 exome

AF:

0.0527

AC:

45712

AN:

866896

Hom.:

3120

Cov.:

AF XY:

0.0522

AC XY:

22921

AN XY:

438950

show subpopulations

Gnomad4 AFR exome

AF:

0.464

Gnomad4 AMR exome

AF:

0.0493

Gnomad4 ASJ exome

AF:

0.104

Gnomad4 EAS exome

AF:

0.000247

Gnomad4 SAS exome

AF:

0.0557

Gnomad4 FIN exome

AF:

0.0234

Gnomad4 NFE exome

AF:

0.0419

Gnomad4 OTH exome

AF:

0.0724

GnomAD4 genome

AF:

0.156

AC:

23702

AN:

152184

Hom.:

4280

Cov.:

AF XY:

0.151

AC XY:

11266

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.444

Gnomad4 AMR

AF:

0.0813

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.00173

Gnomad4 SAS

AF:

0.0562

Gnomad4 FIN

AF:

0.0232

Gnomad4 NFE

AF:

0.0416

Gnomad4 OTH

AF:

0.133

Alfa

AF:

0.0600

Hom.:

685

Bravo

AF:

0.171

Asia WGS

AF:

0.0530

AC:

185

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 22, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.63

DANN

Benign

0.30

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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