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GeneBe

rs2021723

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.09
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 HGVSp Effect #exon/exons MANE UniProt
TRIM40NM_001286633.2 linkuse as main transcriptc.-348G>A 5_prime_UTR_variant 1/6 ENST00000396581.6
TRIM40XM_011514306.2 linkuse as main transcriptc.-535G>A 5_prime_UTR_variant 1/7
TRIM40XM_011514309.2 linkuse as main transcriptc.-669G>A 5_prime_UTR_variant 1/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIM40ENST00000396581.6 linkuse as main transcriptc.-348G>A 5_prime_UTR_variant 1/61 NM_001286633.2 P1Q6P9F5-1
TRIM40ENST00000489892.1 linkuse as main transcriptn.23G>A non_coding_transcript_exon_variant 1/23

Frequencies

GnomAD3 genomes
AF:
0.169
AC:
25647
AN:
152040
Hom.:
2605
Cov.:
32
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:
5
AN:
46
Hom.:
0
Cov.:
0
AF XY:
0.125
AC XY:
4
AN XY:
32
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 EAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0357
Gnomad4 OTH exome
AF:
0.167
GnomAD4 genome
AF:
0.169
AC:
25677
AN:
152158
Hom.:
2608
Cov.:
32
AF XY:
0.166
AC XY:
12328
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.274
Gnomad4 AMR
AF:
0.163
Gnomad4 ASJ
AF:
0.234
Gnomad4 EAS
AF:
0.104
Gnomad4 SAS
AF:
0.161
Gnomad4 FIN
AF:
0.0354
Gnomad4 NFE
AF:
0.128
Gnomad4 OTH
AF:
0.197
Alfa
AF:
0.140
Hom.:
2786
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
12
Dann
Benign
0.60

Splicing

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.

Other links and lift over

dbSNP: rs2021723; hg19: chr6-30103923; API