Variant 5-115126658-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001300759.2(TRIM36):c.1996G>A(p.Asp666Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 1,614,106 control chromosomes in the GnomAD database, including 727,330 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.93 ( 66588 hom., cov: 33)

Exomes 𝑓: 0.95 ( 660742 hom. )

Consequence

TRIM36
NM_001300759.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.376

Variant links:

Genes affected

TRIM36 (HGNC:16280): (tripartite motif containing 36) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

TRIM36 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.14456E-6).

BP6

Variant 5-115126658-C-T is Benign according to our data. Variant chr5-115126658-C-T is described in ClinVar as [Benign]. Clinvar id is 1342267.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM36	NM_001300759.2 linkuse as main transcript	c.1996G>A	p.Asp666Asn	missense_variant	10/10	ENST00000513154.6	NP_001287688.1	Q9NQ86-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRIM36	ENST00000513154.6 linkuse as main transcript	c.1996G>A	p.Asp666Asn	missense_variant	10/10	2	NM_001300759.2	ENSP00000423934.1	Q9NQ86-4
TRIM36	ENST00000282369.7 linkuse as main transcript	c.2032G>A	p.Asp678Asn	missense_variant	10/10	1		ENSP00000282369.3	Q9NQ86-1
TRIM36	ENST00000514154.1 linkuse as main transcript	c.1567G>A	p.Asp523Asn	missense_variant	9/9	1		ENSP00000424259.1	E9PBG3

Frequencies

GnomAD3 genomes

AF:

0.934

AC:

142153

AN:

152150

Hom.:

66533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.882

Gnomad AMI

AF:

0.967

Gnomad AMR

AF:

0.973

Gnomad ASJ

AF:

0.983

Gnomad EAS

AF:

0.921

Gnomad SAS

AF:

0.989

Gnomad FIN

AF:

0.932

Gnomad MID

AF:

0.991

Gnomad NFE

AF:

0.951

Gnomad OTH

AF:

0.959

GnomAD3 exomes

AF:

0.953

AC:

239468

AN:

251244

Hom.:

114269

AF XY:

0.956

AC XY:

129816

AN XY:

135804

show subpopulations

Gnomad AFR exome

AF:

0.883

Gnomad AMR exome

AF:

0.984

Gnomad ASJ exome

AF:

0.985

Gnomad EAS exome

AF:

0.926

Gnomad SAS exome

AF:

0.989

Gnomad FIN exome

AF:

0.932

Gnomad NFE exome

AF:

0.949

Gnomad OTH exome

AF:

0.962

GnomAD4 exome

AF:

0.951

AC:

1389489

AN:

1461838

Hom.:

660742

Cov.:

AF XY:

0.952

AC XY:

692502

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.881

Gnomad4 AMR exome

AF:

0.983

Gnomad4 ASJ exome

AF:

0.985

Gnomad4 EAS exome

AF:

0.908

Gnomad4 SAS exome

AF:

0.988

Gnomad4 FIN exome

AF:

0.931

Gnomad4 NFE exome

AF:

0.949

Gnomad4 OTH exome

AF:

0.957

GnomAD4 genome

AF:

0.934

AC:

142267

AN:

152268

Hom.:

66588

Cov.:

AF XY:

0.936

AC XY:

69705

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.882

Gnomad4 AMR

AF:

0.973

Gnomad4 ASJ

AF:

0.983

Gnomad4 EAS

AF:

0.921

Gnomad4 SAS

AF:

0.989

Gnomad4 FIN

AF:

0.932

Gnomad4 NFE

AF:

0.951

Gnomad4 OTH

AF:

0.959

Alfa

AF:

0.952

Hom.:

178469

Bravo

AF:

0.935

TwinsUK

AF:

0.949

AC:

3519

ALSPAC

AF:

0.943

AC:

3635

ESP6500AA

AF:

0.884

AC:

3894

ESP6500EA

AF:

0.953

AC:

8194

ExAC

AF:

0.949

AC:

115271

Asia WGS

AF:

0.963

AC:

3351

AN:

3478

EpiCase

AF:

0.958

EpiControl

AF:

0.958

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Anencephaly 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.69

CADD

Benign

8.5

DANN

Benign

0.95

DEOGEN2

Benign

0.0046

T;.;T

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.039

LIST_S2

Benign

0.033

T;T;T

MetaRNN

Benign

0.0000021

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

N;.;.

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.28

PROVEAN

Benign

0.79

N;N;N

REVEL

Benign

0.093

Sift

Benign

0.46

T;T;T

Sift4G

Benign

0.67

T;T;T

Polyphen

0.0

B;.;.

Vest4

0.019

MPC

0.046

ClinPred

0.00068

GERP RS

1.0

Varity_R

0.034

gMVP

0.20

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