17-15628756-C-A

Variant names:

• chr17-15628756-C-A
• NM_001348119.1:c.1554G>T
• TRIM16 p.Leu518Leu

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001348119.1(TRIM16):​c.1554G>T​(p.Leu518Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TRIM16 NM_001348119.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 0 publications found

Genes affected

TRIM16 (HGNC:17241): (tripartite motif containing 16) The protein encoded by this gene is a tripartite motif (TRIM) family member that contains two B box domains and a coiled-coiled region that are characteristic of the B box zinc finger protein family. While it lacks a RING domain found in other TRIM proteins, the encoded protein can homodimerize or heterodimerize with other TRIM proteins and has E3 ubiquitin ligase activity. This gene is also a tumor suppressor and is involved in secretory autophagy. [provided by RefSeq, Jan 2017]

ENSG00000251537 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BP7: Synonymous conserved (PhyloP=0.624 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348119.1. 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
	TRIM16	NM_001348119.1	MANE Select	c.1554G>T	p.Leu518Leu	synonymous	Exon 12 of 12	NP_001335048.1	O95361-1
	TRIM16	NM_001348120.1		c.1554G>T	p.Leu518Leu	synonymous	Exon 10 of 10	NP_001335049.1	O95361-1
	TRIM16	NM_006470.4		c.1554G>T	p.Leu518Leu	synonymous	Exon 9 of 9	NP_006461.3	O95361-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM16	ENST00000649191.2	MANE Select	c.1554G>T	p.Leu518Leu	synonymous	Exon 12 of 12	ENSP00000497185.2	O95361-1
	TRIM16	ENST00000336708.11	TSL:1	c.1554G>T	p.Leu518Leu	synonymous	Exon 9 of 9	ENSP00000338989.7	O95361-1
	TRIM16	ENST00000577886.5	TSL:1	c.906G>T	p.Leu302Leu	synonymous	Exon 5 of 5	ENSP00000462903.1	O95361-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	8.6
DANN	Benign	0.84
PhyloP100		0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-15532070;