rs2249099

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007028.5(TRIM31):​c.513+118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,025,500 control chromosomes in the GnomAD database, including 12,704 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 0.13 ( 1481 hom., cov: 32)
Exomes 𝑓: 0.15 ( 11223 hom. )

Consequence

TRIM31
NM_007028.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370
Variant links:
Genes affected
TRIM31 (HGNC:16289): (tripartite motif containing 31) This gene encodes a protein that functions as an E3 ubiquitin-protein ligase. This gene shows altered expression in certain tumors and may be a negative regulator of cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
TRIM31-AS1 (HGNC:39761): (TRIM31 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRIM31NM_007028.5 linkuse as main transcriptc.513+118G>T intron_variant ENST00000376734.4
TRIM31-AS1NR_126470.1 linkuse as main transcriptn.274-188C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIM31ENST00000376734.4 linkuse as main transcriptc.513+118G>T intron_variant 5 NM_007028.5 P1Q9BZY9-1
TRIM31-AS1ENST00000440874.1 linkuse as main transcriptn.274-188C>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.132
AC:
20070
AN:
152036
Hom.:
1471
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0992
Gnomad AMI
AF:
0.173
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.0951
Gnomad EAS
AF:
0.0713
Gnomad SAS
AF:
0.182
Gnomad FIN
AF:
0.150
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.151
Gnomad OTH
AF:
0.113
GnomAD4 exome
AF:
0.153
AC:
133811
AN:
873346
Hom.:
11223
Cov.:
12
AF XY:
0.154
AC XY:
68803
AN XY:
446834
show subpopulations
Gnomad4 AFR exome
AF:
0.0953
Gnomad4 AMR exome
AF:
0.172
Gnomad4 ASJ exome
AF:
0.101
Gnomad4 EAS exome
AF:
0.0883
Gnomad4 SAS exome
AF:
0.184
Gnomad4 FIN exome
AF:
0.148
Gnomad4 NFE exome
AF:
0.158
Gnomad4 OTH exome
AF:
0.150
GnomAD4 genome
AF:
0.132
AC:
20094
AN:
152154
Hom.:
1481
Cov.:
32
AF XY:
0.131
AC XY:
9747
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0991
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.0951
Gnomad4 EAS
AF:
0.0705
Gnomad4 SAS
AF:
0.183
Gnomad4 FIN
AF:
0.150
Gnomad4 NFE
AF:
0.151
Gnomad4 OTH
AF:
0.118
Alfa
AF:
0.150
Hom.:
1050
Bravo
AF:
0.127
Asia WGS
AF:
0.192
AC:
666
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
7.0
DANN
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
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.

Other links and lift over

dbSNP: rs2249099; hg19: chr6-30079307; COSMIC: COSV65059400; COSMIC: COSV65059400; API