7-98987529-G-T

Variant names:

• chr7-98987529-G-T
• rs219818
• NM_001375524.1:c.9390-1236G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375524.1(TRRAP):​c.9390-1236G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,172 control chromosomes in the GnomAD database, including 5,344 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 0.15 (5344 hom., cov: 33)
• Consequence: TRRAP NM_001375524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder with or without congenital anomalies

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• developmental delay with or without dysmorphic facies and autism

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Illumina, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• autosomal dominant nonsyndromic hearing loss

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hearing loss, autosomal dominant 75

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375524.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRRAP	NM_001375524.1	MANE Select	c.9390-1236G>T		intron	N/A	NP_001362453.1
	TRRAP	NM_001244580.2		c.9402-1236G>T		intron	N/A	NP_001231509.1
	TRRAP	NM_003496.4		c.9315-1236G>T		intron	N/A	NP_003487.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRRAP	ENST00000456197.2	TSL:1 MANE Select	c.9390-1236G>T		intron	N/A	ENSP00000394645.2
	TRRAP	ENST00000359863.8	TSL:1	c.9402-1236G>T		intron	N/A	ENSP00000352925.4
	TRRAP	ENST00000355540.7	TSL:1	c.9315-1236G>T		intron	N/A	ENSP00000347733.3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22677 AN: 152054 Hom.: 5324 Cov.: 33

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00393

Gnomad FIN AF: 0.00538

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00757

Gnomad OTH AF: 0.119

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.149 AC: 22746 AN: 152172 Hom.: 5344 Cov.: 33 AF XY: 0.143 AC XY: 10664 AN XY: 74404

African (AFR) AF: 0.502 AC: 20839 AN: 41484

American (AMR) AF: 0.0639 AC: 977 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.00352 AC: 17 AN: 4828

European-Finnish (FIN) AF: 0.00538 AC: 57 AN: 10604

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.00757 AC: 515 AN: 67996

Other (OTH) AF: 0.118 AC: 248 AN: 2108

Alfa AF: 0.0320 Hom.: 1212

Bravo AF: 0.170

Asia WGS AF: 0.0330 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.52
PhyloP100		-0.53
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: rs219818; hg19: chr7-98585152;