X-123671771-TAAAAAA-T

Variant names:

• chrX-123671771-TAAAAAA-T
• NM_001081550.2:c.769-16_769-11delTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001081550.2(THOC2):​c.769-16_769-11delTTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.00000108 in 924,015 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0000011 (0 hom. 0 hem.)
• Consequence: THOC2 NM_001081550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.24

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THOC2	NM_001081550.2	c.769-16_769-11delTTTTTT		intron_variant	Intron 8 of 38	ENST00000245838.13	NP_001075019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THOC2	ENST00000245838.13	c.769-16_769-11delTTTTTT		intron_variant	Intron 8 of 38	5	NM_001081550.2	ENSP00000245838.8
THOC2	ENST00000355725.8	c.769-16_769-11delTTTTTT		intron_variant	Intron 8 of 38	5		ENSP00000347959.4
THOC2	ENST00000491737.5	c.424-16_424-11delTTTTTT		intron_variant	Intron 4 of 33	5		ENSP00000419795.1
THOC2	ENST00000433883.1	n.*399-16_*399-11delTTTTTT		intron_variant	Intron 8 of 9	5		ENSP00000415374.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 0.00000108 AC: 1 AN: 924015 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 271363

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000139

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-122805622;