Genetic Variant TRIM49D2:p.Arg302Gln (chr11-89932431-G-A) – 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_001105522.1(TRIM49D2):c.905G>A(p.Arg302Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TRIM49D2
NM_001105522.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.81

Publications

0 publications found

Variant links:

Genes affected

TRIM49D2 (HGNC:37217): (tripartite motif containing 49D2) 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]

TRIM49D2 links:

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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=0.105599165).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105522.1. 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
	TRIM49D2	NM_001105522.1	MANE Select	c.905G>A	p.Arg302Gln	missense	Exon 7 of 7	NP_001098992.1	C9J1S8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM49D2	ENST00000623787.3	TSL:5 MANE Select	c.905G>A	p.Arg302Gln	missense	Exon 7 of 7	ENSP00000485097.1	C9J1S8
	TRIM49D2	ENST00000526396.3	TSL:5	c.905G>A	p.Arg302Gln	missense	Exon 6 of 6	ENSP00000485325.1	C9J1S8

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

28260

Hom.:

Cov.:

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:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

285942

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

141172

African (AFR)

AF:

0.00

AC:

AN:

1834

American (AMR)

AF:

0.00

AC:

AN:

3094

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4726

East Asian (EAS)

AF:

0.00

AC:

AN:

8450

South Asian (SAS)

AF:

0.00

AC:

AN:

8168

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7452

Middle Eastern (MID)

AF:

0.00

AC:

AN:

838

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

239654

Other (OTH)

AF:

0.00

AC:

AN:

11726

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

28260

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

13690

African (AFR)

AF:

0.00

AC:

AN:

2980

American (AMR)

AF:

0.00

AC:

AN:

2704

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

886

East Asian (EAS)

AF:

0.00

AC:

AN:

1294

South Asian (SAS)

AF:

0.00

AC:

AN:

860

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2370

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

16528

Other (OTH)

AF:

0.00

AC:

AN:

426

Alfa

AF:

0.0000843

Hom.:

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

0.080

BayesDel_addAF

Benign

-0.12

BayesDel_noAF

Benign

-0.42

CADD

Benign

(source)

DANN

Benign

0.62

FATHMM_MKL

Benign

0.0030

LIST_S2

Benign

0.24

MetaRNN

Benign

0.11

PhyloP100

1.8

PrimateAI

Uncertain

0.51

Sift4G

Benign

0.13

Vest4

0.14

MVP

0.030

GERP RS

-1.7

gMVP

0.024

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

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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