rs79213162

Variant names:

• chr16-3694911-C-G
• rs79213162
• NM_016292.3:c.89-3926G>C

Your query was ambiguous. Multiple possible variants found:

• chr16-3694911-C-G
• chr16-3694911-C-T

Variant summary

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

The NM_016292.3(TRAP1):​c.89-3926G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,276 control chromosomes in the GnomAD database, including 200 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 0.048 (200 hom., cov: 31)
• Consequence: TRAP1 NM_016292.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAP1	NM_016292.3	c.89-3926G>C		intron_variant	Intron 1 of 17	ENST00000246957.10	NP_057376.2
TRAP1	NM_001272049.2	c.89-5774G>C		intron_variant	Intron 1 of 16		NP_001258978.1
TRAP1	XM_011522345.3	c.-332-3926G>C		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.89-3926G>C		intron_variant	Intron 1 of 17	1	NM_016292.3	ENSP00000246957.5

Frequencies

GnomAD3 genomes AF: 0.0481 AC: 7316 AN: 152158 Hom.: 200 Cov.: 31

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0751

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0480 AC: 7312 AN: 152276 Hom.: 200 Cov.: 31 AF XY: 0.0494 AC XY: 3679 AN XY: 74458

African (AFR) AF: 0.0226 AC: 938 AN: 41566

American (AMR) AF: 0.0629 AC: 963 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.0353 AC: 183 AN: 5184

South Asian (SAS) AF: 0.0570 AC: 275 AN: 4824

European-Finnish (FIN) AF: 0.0751 AC: 797 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0554 AC: 3766 AN: 68014

Other (OTH) AF: 0.0483 AC: 102 AN: 2112

Alfa AF: 0.0274 Hom.: 9

Bravo AF: 0.0452

Asia WGS AF: 0.0530 AC: 185 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	0.59
DANN	Benign	0.67
PhyloP100		-0.59
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: rs79213162; hg19: chr16-3744912;