Variant X-123671771-TAA-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001081550.2(THOC2):c.769-11del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00343 in 999,454 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000037 ( 0 hom., 0 hem., cov: 23)

Exomes 𝑓: 0.0038 ( 0 hom. 3 hem. )

Consequence

THOC2
NM_001081550.2 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.586

Variant links:

Genes affected

THOC2 (HGNC:19073): (THO complex subunit 2) The TREX multiprotein complex binds specifically to spliced mRNAs to facilitate mRNA export. The protein encoded by this gene is a member of the THO complex, a subset of the TREX complex. The encoded protein interacts with the THOC1 protein.[provided by RefSeq, Jun 2010]

THOC2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Hemizygotes in GnomAdExome4 at 3 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THOC2	NM_001081550.2 linkuse as main transcript	c.769-11del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000245838.13

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
THOC2	ENST00000245838.13 linkuse as main transcript	c.769-11del	splice_polypyrimidine_tract_variant, intron_variant	5	NM_001081550.2	P1	Q8NI27-1
THOC2	ENST00000355725.8 linkuse as main transcript	c.769-11del	splice_polypyrimidine_tract_variant, intron_variant	5		P1	Q8NI27-1
THOC2	ENST00000491737.5 linkuse as main transcript	c.424-11del	splice_polypyrimidine_tract_variant, intron_variant	5
THOC2	ENST00000433883.1 linkuse as main transcript	c.*399-11del	splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0000279

AC:

AN:

107604

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

31354

show subpopulations

Gnomad AFR

AF:

0.0000336

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000388

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00384

AC:

3424

AN:

891818

Hom.:

Cov.:

AF XY:

0.0000117

AC XY:

AN XY:

256168

show subpopulations

Gnomad4 AFR exome

AF:

0.00444

Gnomad4 AMR exome

AF:

0.00834

Gnomad4 ASJ exome

AF:

0.00437

Gnomad4 EAS exome

AF:

0.00282

Gnomad4 SAS exome

AF:

0.00391

Gnomad4 FIN exome

AF:

0.00279

Gnomad4 NFE exome

AF:

0.00373

Gnomad4 OTH exome

AF:

0.00416

GnomAD4 genome

AF:

0.0000372

AC:

AN:

107636

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

31398

show subpopulations

Gnomad4 AFR

AF:

0.0000336

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000388

Gnomad4 OTH

AF:

0.000690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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