chr16-3697203-C-T

Variant names:

• chr16-3697203-C-T
• rs1639150
• NM_016292.3:c.89-6218G>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.89-6218G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,044 control chromosomes in the GnomAD database, including 18,519 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 0.49 (18519 hom., cov: 31)
• Consequence: TRAP1 NM_016292.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAP1	NM_016292.3	c.89-6218G>A		intron_variant	Intron 1 of 17	ENST00000246957.10	NP_057376.2
TRAP1	NM_001272049.2	c.89-8066G>A		intron_variant	Intron 1 of 16		NP_001258978.1
TRAP1	XM_011522345.3	c.-332-6218G>A		intron_variant	Intron 1 of 17		XP_011520647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAP1	ENST00000246957.10	c.89-6218G>A		intron_variant	Intron 1 of 17	1	NM_016292.3	ENSP00000246957.5

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74355 AN: 151926 Hom.: 18503 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.489 AC: 74408 AN: 152044 Hom.: 18519 Cov.: 31 AF XY: 0.496 AC XY: 36852 AN XY: 74350

African (AFR) AF: 0.548 AC: 22726 AN: 41464

American (AMR) AF: 0.507 AC: 7734 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1843 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3213 AN: 5174

South Asian (SAS) AF: 0.588 AC: 2834 AN: 4818

European-Finnish (FIN) AF: 0.518 AC: 5480 AN: 10572

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29072 AN: 67974

Other (OTH) AF: 0.478 AC: 1009 AN: 2112

Alfa AF: 0.450 Hom.: 64980

Bravo AF: 0.489

Asia WGS AF: 0.599 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.62
PhyloP100		-1.6
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: rs1639150; hg19: chr16-3747204;