11-89968654-C-A

Variant names:

• chr11-89968654-C-A
• NM_001136486.2:c.151C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001136486.2(TRIM64):​c.151C>A​(p.Arg51Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R51C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRIM64 NM_001136486.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -2.84
• Publications: 0 publications found

Genes affected

TRIM64 (HGNC:14663): (tripartite motif containing 64) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response; protein ubiquitination; and regulation of gene expression. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.10089743).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136486.2. 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
	TRIM64	NM_001136486.2	MANE Select	c.151C>A	p.Arg51Ser	missense	Exon 2 of 7	NP_001129958.1	A6NGJ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM64	ENST00000533122.4	TSL:1 MANE Select	c.151C>A	p.Arg51Ser	missense	Exon 2 of 7	ENSP00000483764.1	A6NGJ6

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 709448 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 349716

African (AFR) AF: 0.00 AC: 0 AN: 12584

American (AMR) AF: 0.00 AC: 0 AN: 24444

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11446

East Asian (EAS) AF: 0.00 AC: 0 AN: 21644

South Asian (SAS) AF: 0.00 AC: 0 AN: 42728

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1996

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 538660

Other (OTH) AF: 0.00 AC: 0 AN: 28356

GnomAD4 genome Cov.: 0

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	0.17
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	0.038
DANN	Benign	0.52
DEOGEN2	Benign	0.12	T
FATHMM_MKL	Benign	0.0021	N
LIST_S2	Benign	0.18	T
MetaRNN	Benign	0.10	T
MutationAssessor	Benign	-0.47	N
PhyloP100		-2.8
PrimateAI	Benign	0.37	T
Sift4G	Benign	0.43	T
Polyphen		0.0080	B
Vest4		0.057
MVP		0.014
GERP RS		-2.3
PromoterAI		0.014	Neutral
Varity_R		0.12
gMVP		0.025

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

hg19: chr11-89701822;