Variant chr1-33165468-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018207.3(TRIM62):c.504+3G>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,593,538 control chromosomes in the GnomAD database, including 44,425 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 0.20 ( 3226 hom., cov: 32)

Exomes 𝑓: 0.24 ( 41199 hom. )

Consequence

TRIM62
NM_018207.3 splice_donor_region, intron

Scores

Splicing: ADA: 0.9927

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34

Variant links:

Genes affected

TRIM62 (HGNC:25574): (tripartite motif containing 62) Enables identical protein binding activity; transcription coactivator activity; and ubiquitin-protein transferase activity. Involved in several processes, including negative regulation of viral transcription; positive regulation of NF-kappaB transcription factor activity; and positive regulation of antifungal innate immune response. Is active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TRIM62 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
TRIM62	NM_018207.3 linkuse as main transcript	c.504+3G>T	splice_donor_region_variant, intron_variant		ENST00000291416.10
AZIN2	XM_047443457.1 linkuse as main transcript	c.*4503C>A	3_prime_UTR_variant	10/10
TRIM62	NM_001330483.2 linkuse as main transcript	c.141+3G>T	splice_donor_region_variant, intron_variant
ZNF362	XM_047447108.1 linkuse as main transcript	c.-24+37019C>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM62	ENST00000291416.10 linkuse as main transcript	c.504+3G>T	splice_donor_region_variant, intron_variant		1	NM_018207.3	P1	Q9BVG3-1
	ENST00000624339.1 linkuse as main transcript	n.2618C>A	non_coding_transcript_exon_variant	1/1
TRIM62	ENST00000543586.1 linkuse as main transcript	c.141+3G>T	splice_donor_region_variant, intron_variant		2			Q9BVG3-2
TRIM62	ENST00000485148.1 linkuse as main transcript	n.553+3G>T	splice_donor_region_variant, intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29806

AN:

152120

Hom.:

3229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0897

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.217

GnomAD3 exomes

AF:

0.228

AC:

50973

AN:

223550

Hom.:

6139

AF XY:

0.236

AC XY:

28561

AN XY:

120914

show subpopulations

Gnomad AFR exome

AF:

0.0876

Gnomad AMR exome

AF:

0.181

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.215

Gnomad SAS exome

AF:

0.309

Gnomad FIN exome

AF:

0.255

Gnomad NFE exome

AF:

0.238

Gnomad OTH exome

AF:

0.224

GnomAD4 exome

AF:

0.236

AC:

340164

AN:

1441300

Hom.:

41199

Cov.:

AF XY:

0.239

AC XY:

170793

AN XY:

715510

show subpopulations

Gnomad4 AFR exome

AF:

0.0845

Gnomad4 AMR exome

AF:

0.184

Gnomad4 ASJ exome

AF:

0.222

Gnomad4 EAS exome

AF:

0.199

Gnomad4 SAS exome

AF:

0.310

Gnomad4 FIN exome

AF:

0.255

Gnomad4 NFE exome

AF:

0.238

Gnomad4 OTH exome

AF:

0.223

GnomAD4 genome

AF:

0.196

AC:

29810

AN:

152238

Hom.:

3226

Cov.:

AF XY:

0.199

AC XY:

14816

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0898

Gnomad4 AMR

AF:

0.202

Gnomad4 ASJ

AF:

0.214

Gnomad4 EAS

AF:

0.213

Gnomad4 SAS

AF:

0.298

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.225

Hom.:

5176

Bravo

AF:

0.184

Asia WGS

AF:

0.208

AC:

721

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Benign

0.96

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

0.99

dbscSNV1_RF

Pathogenic

0.81

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over