Genetic Variant TRIM40:c.-348G>A (chr6-30136146-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001286633.2(TRIM40):c.-348G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,204 control chromosomes in the GnomAD database, including 2,608 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2608 hom., cov: 32)

Exomes 𝑓: 0.11 ( 0 hom. )

Consequence

TRIM40
NM_001286633.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.09

Publications

24 publications found

Variant links:

Genes affected

TRIM40 (HGNC:18736): (tripartite motif containing 40) This gene encodes a member of the tripartite motif (TRIM) protein family. The encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]

TRIM40 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TRIM40	NM_001286633.2 link	c.-348G>A	5_prime_UTR_variant	Exon 1 of 6	ENST00000396581.6	NP_001273562.1	Q6P9F5-1A0A1U9X8U1
TRIM40	XM_011514306.2 link	c.-535G>A	5_prime_UTR_variant	Exon 1 of 7		XP_011512608.1	Q6P9F5-1A0A1U9X8U1
TRIM40	XM_011514309.2 link	c.-669G>A	5_prime_UTR_variant	Exon 1 of 5		XP_011512611.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM40	ENST00000396581.6 link	c.-348G>A		5_prime_UTR_variant	Exon 1 of 6	1	NM_001286633.2	ENSP00000379826.1		Q6P9F5-1
TRIM40	ENST00000489892.1 link	n.23G>A		non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25647

AN:

152040

Hom.:

2605

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0354

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.200

GnomAD4 exome

AF:

0.109

AC:

AN:

Hom.:

Cov.:

AF XY:

0.125

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0357

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.169

AC:

25677

AN:

152158

Hom.:

2608

Cov.:

AF XY:

0.166

AC XY:

12328

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.274

AC:

11354

AN:

41484

American (AMR)

AF:

0.163

AC:

2497

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

812

AN:

3464

East Asian (EAS)

AF:

0.104

AC:

536

AN:

5178

South Asian (SAS)

AF:

0.161

AC:

774

AN:

4814

European-Finnish (FIN)

AF:

0.0354

AC:

376

AN:

10608

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8729

AN:

68004

Other (OTH)

AF:

0.197

AC:

416

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1059

2117

3176

4234

5293

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.143

Hom.:

6814

Bravo

AF:

0.188

Asia WGS

AF:

0.122

AC:

426

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

1.1

PromoterAI

-0.035

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over