Variant chr1-231606829-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000602956.5(TSNAX-DISC1):n.495+45574T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,112 control chromosomes in the GnomAD database, including 41,301 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 0.73 ( 41301 hom., cov: 31)

Consequence

TSNAX-DISC1
ENST00000602956.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.854

Variant links:

Genes affected

TSNAX-DISC1 (HGNC:49177): (TSNAX-DISC1 readthrough (NMD candidate)) This gene represents naturally occurring read-through transcription between the neighboring TSNAX (translin-associated factor X) and DISC1 (disrupted in schizophrenia 1) genes on chromosome 1. Alternative splicing results in multiple transcript variants, all of which are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to be protein-coding. These alterations in gene processing may be associated with risk for psychiatric illness, most notably, schizophrenia. [provided by RefSeq, Nov 2010]

TSNAX-DISC1 links:

LINC00582 (HGNC:43842): (long intergenic non-protein coding RNA 582)

LINC00582 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
TSNAX-DISC1	NR_028393.1 link	n.526-9815T>C	intron_variant
TSNAX-DISC1	NR_028394.1 link	n.654-9815T>C	intron_variant
TSNAX-DISC1	NR_028395.1 link	n.654-9815T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSNAX-DISC1	ENST00000602956.5 link	n.495+45574T>C		intron_variant		2		ENSP00000473532.1		C4P0D8

Frequencies

GnomAD3 genomes

AF:

0.731

AC:

111104

AN:

151992

Hom.:

41259

Cov.:

show subpopulations

Gnomad AFR

AF:

0.633

Gnomad AMI

AF:

0.876

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.767

Gnomad EAS

AF:

0.534

Gnomad SAS

AF:

0.833

Gnomad FIN

AF:

0.775

Gnomad MID

AF:

0.845

Gnomad NFE

AF:

0.807

Gnomad OTH

AF:

0.737

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

GnomAD4 genome

AF:

0.731

AC:

111198

AN:

152112

Hom.:

41301

Cov.:

AF XY:

0.728

AC XY:

54145

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.633

Gnomad4 AMR

AF:

0.642

Gnomad4 ASJ

AF:

0.767

Gnomad4 EAS

AF:

0.535

Gnomad4 SAS

AF:

0.833

Gnomad4 FIN

AF:

0.775

Gnomad4 NFE

AF:

0.807

Gnomad4 OTH

AF:

0.739

Alfa

AF:

0.790

Hom.:

62821

Bravo

AF:

0.714

Asia WGS

AF:

0.721

AC:

2510

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.0

DANN

Benign

0.65

Splicing

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