rs1639150

Positions:

• chr16-3697203-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TRAP1	NM_016292.3	c.89-6218G>A		intron_variant		ENST00000246957.10	NP_057376.2
TRAP1	NM_001272049.2	c.89-8066G>A		intron_variant			NP_001258978.1
TRAP1	XM_011522345.3	c.-332-6218G>A		intron_variant			XP_011520647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAP1	ENST00000246957.10	c.89-6218G>A		intron_variant		1	NM_016292.3	ENSP00000246957	P1

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

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.478

Alfa AF: 0.443 Hom.: 32619

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

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

Other links and lift over

dbSNP: rs1639150; hg19: chr16-3747204;