rs2108430

Positions:

• chr16-3688077-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.330+978G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,880 control chromosomes in the GnomAD database, including 11,712 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 0.37 (11712 hom., cov: 30)
• Consequence: TRAP1 NM_016292.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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]

TRAP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAP1	NM_016292.3	c.330+978G>A		intron_variant		ENST00000246957.10	NP_057376.2
TRAP1	NM_001272049.2	c.171+978G>A		intron_variant			NP_001258978.1
TRAP1	XM_011522345.3	c.-91+978G>A		intron_variant			XP_011520647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAP1	ENST00000246957.10	c.330+978G>A		intron_variant		1	NM_016292.3	ENSP00000246957.5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55678 AN: 151762 Hom.: 11683 Cov.: 30

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.367 AC: 55775 AN: 151880 Hom.: 11712 Cov.: 30 AF XY: 0.365 AC XY: 27100 AN XY: 74224

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.372

Alfa AF: 0.331 Hom.: 1163

Bravo AF: 0.384

Asia WGS AF: 0.395 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.32

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: rs2108430; hg19: chr16-3738078;