Genetic Variant NM_001136486.2:c.1052A>G (chr11-89973591-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

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

The NM_001136486.2(TRIM64):c.1052A>G(p.Asn351Ser) 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 (★).

Frequency

Genomes: 𝑓 0.000050 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0000040 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

TRIM64
NM_001136486.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.05

Publications

0 publications found

Variant links:

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]

TRIM64 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.09898457).

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.1052A>G	p.Asn351Ser	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.1052A>G	p.Asn351Ser	missense	Exon 7 of 7	ENSP00000483764.1	A6NGJ6

Frequencies

GnomAD3 genomes

AF:

0.0000502

AC:

AN:

39858

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000536

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000381

AC:

AN:

52486

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000351

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000403

AC:

AN:

495720

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

244518

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6552

American (AMR)

AF:

0.000229

AC:

AN:

8718

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9426

East Asian (EAS)

AF:

0.00

AC:

AN:

10692

South Asian (SAS)

AF:

0.00

AC:

AN:

25248

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21504

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1568

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

391508

Other (OTH)

AF:

0.00

AC:

AN:

20504

GnomAD4 genome

AF:

0.0000502

AC:

AN:

39858

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

19514

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6626

American (AMR)

AF:

0.00

AC:

AN:

3602

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1184

East Asian (EAS)

AF:

0.00

AC:

AN:

1432

South Asian (SAS)

AF:

0.00

AC:

AN:

1024

European-Finnish (FIN)

AF:

0.000536

AC:

AN:

3730

Middle Eastern (MID)

AF:

0.00

AC:

AN:

112

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

21342

Other (OTH)

AF:

0.00

AC:

AN:

588

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.098

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.013

(source)

DANN

Benign

0.22

DEOGEN2

Benign

0.074

FATHMM_MKL

Benign

0.0019

LIST_S2

Benign

0.69

MetaRNN

Benign

0.099

MutationAssessor

Benign

0.10

PhyloP100

-2.1

PrimateAI

Benign

0.39

Sift4G

Benign

0.20

Polyphen

0.050

Vest4

0.089

MVP

0.067

GERP RS

-2.8

Varity_R

0.040

gMVP

0.0028

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over