chr6-30149324-T-C

Variant names:

• chr6-30149324-T-C
• rs9261519
• ENST00000883266.1:c.*1512T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000883266.1(TRIM40):​c.*1512T>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 0.22 in 152,150 control chromosomes in the GnomAD database, including 4,028 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 0.22 (4028 hom., cov: 32)
• Consequence: TRIM40 ENST00000883266.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 23 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000883266.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM40	ENST00000883266.1		c.*1512T>C		3_prime_UTR	Exon 7 of 7	ENSP00000553325.1

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33466 AN: 152030 Hom.: 4026 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.189

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.220 AC: 33485 AN: 152150 Hom.: 4028 Cov.: 32 AF XY: 0.222 AC XY: 16480 AN XY: 74380

African (AFR) AF: 0.144 AC: 5992 AN: 41514

American (AMR) AF: 0.257 AC: 3922 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1280 AN: 5178

South Asian (SAS) AF: 0.126 AC: 608 AN: 4812

European-Finnish (FIN) AF: 0.310 AC: 3288 AN: 10598

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17074 AN: 67990

Other (OTH) AF: 0.187 AC: 394 AN: 2106

Alfa AF: 0.228 Hom.: 6220

Bravo AF: 0.213

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.61
PhyloP100		-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9261519; hg19: chr6-30117101;