rs72778151

Variant names:

• chr16-3688285-G-T
• rs72778151
• NM_016292.3:c.330+770C>A

Variant summary

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

The NM_016292.3(TRAP1):​c.330+770C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,844 control chromosomes in the GnomAD database, including 2,561 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 0.18 (2561 hom., cov: 30)
• Consequence: TRAP1 NM_016292.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 5 publications found

Genes affected

TRAP1 (HGNC:16264): (TNF receptor associated protein 1) This gene encodes a mitochondrial chaperone protein that is member of the heat shock protein 90 (HSP90) family. The encoded protein has ATPase activity and interacts with tumor necrosis factor type I. This protein may function in regulating cellular stress responses. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

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 (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAP1	NM_016292.3	c.330+770C>A		intron_variant	Intron 3 of 17	ENST00000246957.10	NP_057376.2
TRAP1	NM_001272049.2	c.171+770C>A		intron_variant	Intron 2 of 16		NP_001258978.1
TRAP1	XM_011522345.3	c.-91+770C>A		intron_variant	Intron 3 of 17		XP_011520647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAP1	ENST00000246957.10	c.330+770C>A		intron_variant	Intron 3 of 17	1	NM_016292.3	ENSP00000246957.5

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27436 AN: 151726 Hom.: 2555 Cov.: 30

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.181 AC: 27479 AN: 151844 Hom.: 2561 Cov.: 30 AF XY: 0.181 AC XY: 13396 AN XY: 74196

African (AFR) AF: 0.184 AC: 7633 AN: 41372

American (AMR) AF: 0.144 AC: 2202 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1039 AN: 5152

South Asian (SAS) AF: 0.187 AC: 900 AN: 4802

European-Finnish (FIN) AF: 0.146 AC: 1540 AN: 10548

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12691 AN: 67934

Other (OTH) AF: 0.189 AC: 397 AN: 2106

Alfa AF: 0.183 Hom.: 985

Bravo AF: 0.180

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs72778151; hg19: chr16-3738286;