dbSNP rs1573298: TRIM40:c.*571G>C (chr6-30148383-G-C) – 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.*571G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 163,216 control chromosomes in the GnomAD database, including 4,550 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 0.23 ( 4302 hom., cov: 32)

Exomes 𝑓: 0.20 ( 248 hom. )

Consequence

TRIM40
NM_001286633.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145

Publications

18 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:

Genome browser will be placed here

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TRIM40	NM_001286633.2 link	c.*571G>C	3_prime_UTR_variant	Exon 6 of 6	ENST00000396581.6	NP_001273562.1	Q6P9F5-1A0A1U9X8U1
TRIM40	NM_138700.4 link	c.*571G>C	3_prime_UTR_variant	Exon 5 of 5		NP_619645.1	Q6P9F5-2
TRIM40	XM_011514306.2 link	c.*571G>C	3_prime_UTR_variant	Exon 7 of 7		XP_011512608.1	Q6P9F5-1A0A1U9X8U1
TRIM40	XM_011514309.2 link	c.*602G>C	3_prime_UTR_variant	Exon 5 of 5		XP_011512611.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TRIM40	ENST00000396581.6 link	c.*571G>C	3_prime_UTR_variant	Exon 6 of 6	1	NM_001286633.2	ENSP00000379826.1	Q6P9F5-1
TRIM40	ENST00000307859.4 link	c.*571G>C	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000308310.4	Q6P9F5-2
TRIM40	ENST00000376724.6 link	c.*571G>C	3_prime_UTR_variant	Exon 5 of 5	2		ENSP00000365914.2	Q6P9F5-1

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34674

AN:

152018

Hom.:

4294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.257

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.203

GnomAD4 exome

AF:

0.205

AC:

2266

AN:

11078

Hom.:

248

Cov.:

AF XY:

0.204

AC XY:

1187

AN XY:

5832

show subpopulations

African (AFR)

AF:

0.0971

AC:

AN:

206

American (AMR)

AF:

0.209

AC:

498

AN:

2386

Ashkenazi Jewish (ASJ)

AF:

0.0846

AC:

AN:

130

East Asian (EAS)

AF:

0.172

AC:

125

AN:

726

South Asian (SAS)

AF:

0.218

AC:

269

AN:

1232

European-Finnish (FIN)

AF:

0.217

AC:

AN:

152

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.212

AC:

1226

AN:

5772

Other (OTH)

AF:

0.183

AC:

AN:

458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

169

253

338

422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

192

240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.228

AC:

34702

AN:

152138

Hom.:

4302

Cov.:

AF XY:

0.232

AC XY:

17227

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.146

AC:

6041

AN:

41516

American (AMR)

AF:

0.261

AC:

3983

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

707

AN:

3466

East Asian (EAS)

AF:

0.270

AC:

1396

AN:

5170

South Asian (SAS)

AF:

0.257

AC:

1238

AN:

4820

European-Finnish (FIN)

AF:

0.311

AC:

3285

AN:

10574

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.254

AC:

17283

AN:

67990

Other (OTH)

AF:

0.208

AC:

439

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1373

2746

4119

5492

6865

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.243

Hom.:

595

Bravo

AF:

0.217

Asia WGS

AF:

0.283

AC:

984

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.2

(source)

DANN

Benign

0.55

PhyloP100

-0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over