16-3695272-G-A

Position:

• chr16-3695272-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016292.3(TRAP1):​c.89-4287C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,184 control chromosomes in the GnomAD database, including 1,339 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 0.11 (1339 hom., cov: 31)
• Consequence: TRAP1 NM_016292.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAP1	NM_016292.3	c.89-4287C>T		intron_variant		ENST00000246957.10
TRAP1	NM_001272049.2	c.89-6135C>T		intron_variant
TRAP1	XM_011522345.3	c.-332-4287C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAP1	ENST00000246957.10	c.89-4287C>T		intron_variant		1	NM_016292.3	P1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17243 AN: 152066 Hom.: 1337 Cov.: 31

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.113 AC: 17238 AN: 152184 Hom.: 1339 Cov.: 31 AF XY: 0.111 AC XY: 8294 AN XY: 74400

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.117

Alfa AF: 0.150 Hom.: 384

Bravo AF: 0.106

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.47

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: rs75712687; hg19: chr16-3745273;