Genetic Variant ENST00000412903.1:c.-334T>G (chr11-5938527-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412903.1(TRIM5):c.-334T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,896 control chromosomes in the GnomAD database, including 7,431 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 0.30 ( 7431 hom., cov: 31)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

TRIM5
ENST00000412903.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20

Publications

7 publications found

Variant links:

Genes affected

TRIM5 (HGNC:16276): (tripartite motif containing 5) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein forms homo-oligomers via the coilel-coil region and localizes to cytoplasmic bodies. It appears to function as a E3 ubiquitin-ligase and ubiqutinates itself to regulate its subcellular localization. It may play a role in retroviral restriction. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2009]

TRIM5 links:

LOC112268071 (HGNC:):

LOC112268071 links:

OR56A3 (HGNC:14786): (olfactory receptor family 56 subfamily A member 3) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

OR56A3 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC112268071	XR_002957230.2 link	n.95T>G	non_coding_transcript_exon_variant	Exon 1 of 3
LOC112268071	XR_002957231.2 link	n.95T>G	non_coding_transcript_exon_variant	Exon 1 of 3
LOC112268071	XR_002957234.2 link	n.95T>G	non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM5	ENST00000412903.1 link	c.-334T>G		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000388031.1		E7EQQ5
OR56A3	ENST00000528915.1 link	n.-224A>C		upstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46178

AN:

151766

Hom.:

7413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.402

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.200

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.200

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.608

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.304

AC:

46240

AN:

151884

Hom.:

7431

Cov.:

AF XY:

0.303

AC XY:

22464

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.402

AC:

16648

AN:

41386

American (AMR)

AF:

0.290

AC:

4434

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

804

AN:

3466

East Asian (EAS)

AF:

0.246

AC:

1260

AN:

5130

South Asian (SAS)

AF:

0.241

AC:

1163

AN:

4820

European-Finnish (FIN)

AF:

0.292

AC:

3083

AN:

10552

Middle Eastern (MID)

AF:

0.271

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.264

AC:

17949

AN:

67938

Other (OTH)

AF:

0.294

AC:

619

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

1523

3046

4569

6092

7615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.271

Hom.:

10486

Bravo

AF:

0.308

Asia WGS

AF:

0.264

AC:

918

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.9

(source)

DANN

Benign

0.55

PhyloP100

-2.2

PromoterAI

-0.0031

Neutral

(source)

Splicing

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

Publications

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ENST00000412903.1:c.-334T>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over