rs3132676

chr6-30148301-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286633.2(TRIM40):c.*489A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 172,962 control chromosomes in the GnomAD database, including 65,140 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 0.87 (57312 hom., cov: 31)
  • Exomes 𝑓: 0.87 (7828 hom.)
• Consequence: TRIM40 NM_001286633.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM40	NM_001286633.2	c.*489A>G		3_prime_UTR_variant	6/6	ENST00000396581.6
TRIM40	NM_138700.4	c.*489A>G		3_prime_UTR_variant	5/5
TRIM40	XM_011514306.2	c.*489A>G		3_prime_UTR_variant	7/7
TRIM40	XM_011514309.2	c.*520A>G		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM40	ENST00000396581.6	c.*489A>G		3_prime_UTR_variant	6/6	1	NM_001286633.2	P1
TRIM40	ENST00000307859.4	c.*489A>G		3_prime_UTR_variant	5/5	1
TRIM40	ENST00000376724.6	c.*489A>G		3_prime_UTR_variant	5/5	2		P1

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131833 AN: 152126 Hom.: 57262 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.865

GnomAD4 exome AF: 0.866 AC: 17950 AN: 20718 Hom.: 7828 Cov.: 0 AF XY: 0.869 AC XY: 9336 AN XY: 10746

Gnomad4 AFR exome AF: 0.874

Gnomad4 AMR exome AF: 0.905

Gnomad4 ASJ exome AF: 0.923

Gnomad4 EAS exome AF: 0.986

Gnomad4 SAS exome AF: 0.912

Gnomad4 FIN exome AF: 0.808

Gnomad4 NFE exome AF: 0.834

Gnomad4 OTH exome AF: 0.837

GnomAD4 genome AF: 0.867 AC: 131943 AN: 152244 Hom.: 57312 Cov.: 31 AF XY: 0.868 AC XY: 64628 AN XY: 74444

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.867

Alfa AF: 0.858 Hom.: 99062

Bravo AF: 0.871

Asia WGS AF: 0.948 AC: 3298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.17
Dann	Benign	0.66

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

LitVar

Other links and lift over

dbSNP: rs3132676; hg19: chr6-30116078;