Variant 11-55885495-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032681.4(TRIM51):c.67C>A(p.Leu23Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.985 in 152,216 control chromosomes in the GnomAD database, including 73,833 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.98 ( 73833 hom., cov: 31)

Exomes 𝑓: 0.99 ( 702026 hom. )

Failed GnomAD Quality Control

Consequence

TRIM51
NM_032681.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0970

Variant links:

Genes affected

TRIM51 (HGNC:19023): (tripartite motif-containing 51) 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]

TRIM51 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.2290616E-6).

BP6

Variant 11-55885495-C-A is Benign according to our data. Variant chr11-55885495-C-A is described in ClinVar as [Benign]. Clinvar id is 768449.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM51	NM_032681.4 linkuse as main transcript	c.67C>A	p.Leu23Ile	missense_variant	2/7	ENST00000449290.6	NP_116070.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM51	ENST00000449290.6 linkuse as main transcript	c.67C>A	p.Leu23Ile	missense_variant	2/7	5	NM_032681.4	ENSP00000395086	P1	Q9BSJ1-1

Frequencies

GnomAD3 genomes

AF:

0.985

AC:

149767

AN:

152098

Hom.:

73776

Cov.:

show subpopulations

Gnomad AFR

AF:

0.947

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.994

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.988

GnomAD3 exomes

AF:

0.991

AC:

245775

AN:

248032

Hom.:

121777

AF XY:

0.992

AC XY:

133618

AN XY:

134726

show subpopulations

Gnomad AFR exome

AF:

0.945

Gnomad AMR exome

AF:

0.994

Gnomad ASJ exome

AF:

0.999

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.997

Gnomad FIN exome

AF:

0.996

Gnomad NFE exome

AF:

0.991

Gnomad OTH exome

AF:

0.992

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.987

AC:

1422220

AN:

1440500

Hom.:

702026

Cov.:

AF XY:

0.988

AC XY:

708444

AN XY:

717084

show subpopulations

Gnomad4 AFR exome

AF:

0.947

Gnomad4 AMR exome

AF:

0.995

Gnomad4 ASJ exome

AF:

0.998

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.997

Gnomad4 FIN exome

AF:

0.999

Gnomad4 NFE exome

AF:

0.986

Gnomad4 OTH exome

AF:

0.988

GnomAD4 genome

AF:

0.985

AC:

149882

AN:

152216

Hom.:

73833

Cov.:

AF XY:

0.985

AC XY:

73318

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.947

Gnomad4 AMR

AF:

0.995

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

1.00

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

1.00

Gnomad4 OTH

AF:

0.988

Alfa

AF:

0.994

Hom.:

30456

Bravo

AF:

0.983

ExAC

AF:

0.985

AC:

119059

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 24, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.10

DANN

Benign

0.55

DEOGEN2

Benign

0.0033

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.00023

LIST_S2

Benign

0.026

MetaRNN

Benign

0.0000012

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.36

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.50

PROVEAN

Benign

0.45

REVEL

Benign

0.057

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.032

MPC

0.084

ClinPred

0.00087

GERP RS

0.80

Varity_R

0.050

gMVP

0.034

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over