chr6-30148301-A-G

Variant names:

• chr6-30148301-A-G
• rs3132676
• NM_001286633.2:c.*489A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIM40	NM_001286633.2	c.*489A>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000396581.6	NP_001273562.1
TRIM40	NM_138700.4	c.*489A>G		3_prime_UTR_variant	Exon 5 of 5		NP_619645.1
TRIM40	XM_011514306.2	c.*489A>G		3_prime_UTR_variant	Exon 7 of 7		XP_011512608.1
TRIM40	XM_011514309.2	c.*520A>G		3_prime_UTR_variant	Exon 5 of 5		XP_011512611.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM40	ENST00000396581.6	c.*489A>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_001286633.2	ENSP00000379826.1
TRIM40	ENST00000307859.4	c.*489A>G		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000308310.4
TRIM40	ENST00000376724.6	c.*489A>G		3_prime_UTR_variant	Exon 5 of 5	2		ENSP00000365914.2

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

African (AFR) AF: 0.874 AC: 484 AN: 554

American (AMR) AF: 0.905 AC: 2819 AN: 3114

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 382 AN: 414

East Asian (EAS) AF: 0.986 AC: 1398 AN: 1418

South Asian (SAS) AF: 0.912 AC: 2051 AN: 2248

European-Finnish (FIN) AF: 0.808 AC: 357 AN: 442

Middle Eastern (MID) AF: 0.868 AC: 59 AN: 68

European-Non Finnish (NFE) AF: 0.834 AC: 9575 AN: 11474

Other (OTH) AF: 0.837 AC: 825 AN: 986

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

African (AFR) AF: 0.869 AC: 36086 AN: 41538

American (AMR) AF: 0.892 AC: 13638 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3184 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5123 AN: 5184

South Asian (SAS) AF: 0.925 AC: 4465 AN: 4826

European-Finnish (FIN) AF: 0.862 AC: 9146 AN: 10612

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57353 AN: 68006

Other (OTH) AF: 0.867 AC: 1834 AN: 2116

Alfa AF: 0.858 Hom.: 228442

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
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3132676; hg19: chr6-30116078;