chr11-89973612-A-G

Variant names:

• chr11-89973612-A-G
• rs4572095
• NM_001136486.2:c.1073A>G

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001136486.2(TRIM64):​c.1073A>G​(p.Gln358Arg) 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 Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRIM64 NM_001136486.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.647
• 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 -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.022571534).
• BP6: Variant 11-89973612-A-G is Benign according to our data. Variant chr11-89973612-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3810602.Status of the report is criteria_provided_single_submitter, 1 stars.

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.1073A>G	p.Gln358Arg	missense	Exon 7 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.1073A>G	p.Gln358Arg	missense	Exon 7 of 7	ENSP00000483764.1	A6NGJ6

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.0000760 AC: 4 AN: 52662 AF XY: 0.000142

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000882

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 495814 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 244574

African (AFR) AF: 0.00 AC: 0 AN: 6548

American (AMR) AF: 0.00 AC: 0 AN: 8720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9426

East Asian (EAS) AF: 0.00 AC: 0 AN: 10692

South Asian (SAS) AF: 0.00 AC: 0 AN: 25256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21508

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1638

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 391516

Other (OTH) AF: 0.00 AC: 0 AN: 20510

GnomAD4 genome Cov.: 0

ClinVar

ClinVar submissions

Significance: Likely benign

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	0.068
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	0.20
DANN	Benign	0.26
DEOGEN2	Benign	0.0052	T
FATHMM_MKL	Benign	0.0060	N
LIST_S2	Benign	0.057	T
MetaRNN	Benign	0.023	T
MutationAssessor	Benign	-1.7	N
PhyloP100		0.65
PrimateAI	Benign	0.36	T
Sift4G	Benign	0.43	T
Polyphen		0.0	B
Vest4		0.067
MVP		0.061
GERP RS		-1.5
Varity_R		0.028
gMVP		0.0093

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: rs4572095; hg19: chr11-89706780;