17-18732068-G-A

Variant names:

• chr17-18732068-G-A
• rs2034684115
• ENST00000571708.5:n.1023G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000571708.5(TRIM16L):​n.1023G>A variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: TRIM16L ENST00000571708.5 non_coding_transcript_exon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.97
• Publications: 0 publications found

Genes affected

TRIM16L (HGNC:):

TRIM16L (HGNC:32670): (tripartite motif containing 16 like (pseudogene)) Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15200159).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000571708.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM16L	NR_172633.1		n.1103G>A		non_coding_transcript_exon	Exon 9 of 10
	TRIM16L	NR_172634.1		n.952G>A		non_coding_transcript_exon	Exon 8 of 9
	TRIM16L	NR_172635.1		n.854G>A		non_coding_transcript_exon	Exon 7 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM16L	ENST00000571708.5	TSL:1	n.1023G>A		non_coding_transcript_exon	Exon 9 of 10
	TRIM16L	ENST00000424146.3	TSL:3	n.476G>A		non_coding_transcript_exon	Exon 3 of 4
	TRIM16L	ENST00000449552.6	TSL:2	n.1881G>A		non_coding_transcript_exon	Exon 6 of 7

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.053	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	17
DANN	Benign	0.81
DEOGEN2	Benign	0.0079	T
Eigen	Benign	0.0093
Eigen_PC	Benign	0.0040
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.69	T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-0.60	T
MutationAssessor	Uncertain	2.6	M
PhyloP100		4.0
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.25	N
REVEL	Benign	0.082
Sift	Benign	0.43	T
Sift4G	Benign	0.15	T
Polyphen		0.57	P
Vest4		0.11
MutPred		0.35		Gain of phosphorylation at A133 (P = 0.06)
MVP		0.59
ClinPred		0.45	T
GERP RS		3.3
Varity_R		0.061
gMVP		0.26

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: rs2034684115; hg19: chr17-18635381;