chr1-155179017-C-T

Variant names:

• chr1-155179017-C-T
• rs11264341
• NM_025058.5:c.1285+404C>T

Variant summary

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

The NM_025058.5(TRIM46):​c.1285+404C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,158 control chromosomes in the GnomAD database, including 13,351 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 0.41 (13351 hom., cov: 33)
• Consequence: TRIM46 NM_025058.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41
• Publications: 64 publications found

Genes affected

TRIM46 (HGNC:19019): (tripartite motif containing 46) This gene encodes a protein of the tripartite motif (TRIM) family. The TRIM motif includes zinc-binding domains, a RING finger region, a B-box motif and a coiled-coil domain. TRIM46 is reported to be involved in the proliferation of multiple types of cancer cells including lung and breast cancer. It has also been shown to control neuronal polarity and axon specification by forming uniform microtubule bundles in the axon. [provided by RefSeq, May 2022]

ENSG00000273088 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM46	NM_025058.5	c.1285+404C>T		intron_variant	Intron 7 of 9	ENST00000334634.9	NP_079334.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM46	ENST00000334634.9	c.1285+404C>T		intron_variant	Intron 7 of 9	1	NM_025058.5	ENSP00000334657.4
ENSG00000273088	ENST00000473363.3	c.49-5543G>A		intron_variant	Intron 1 of 4	5		ENSP00000477381.3

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61792 AN: 152040 Hom.: 13353 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.406 AC: 61807 AN: 152158 Hom.: 13351 Cov.: 33 AF XY: 0.413 AC XY: 30730 AN XY: 74384

African (AFR) AF: 0.272 AC: 11276 AN: 41522

American (AMR) AF: 0.538 AC: 8220 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1341 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3701 AN: 5164

South Asian (SAS) AF: 0.466 AC: 2253 AN: 4830

European-Finnish (FIN) AF: 0.473 AC: 5004 AN: 10582

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28721 AN: 67990

Other (OTH) AF: 0.419 AC: 884 AN: 2110

Alfa AF: 0.419 Hom.: 48995

Bravo AF: 0.410

Asia WGS AF: 0.527 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.35
DANN	Benign	0.71
PhyloP100		-3.4
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: rs11264341; hg19: chr1-155151493; COSMIC: COSV58118961; COSMIC: COSV58118961;