chr1-231596610-G-A

Position:

• chr1-231596610-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602956.5(TSNAX-DISC1):​n.495+35355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,962 control chromosomes in the GnomAD database, including 17,106 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 0.45 (17106 hom., cov: 31)
• Consequence: TSNAX-DISC1 ENST00000602956.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87

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]

LINC00582 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSNAX-DISC1	NR_028393.1	n.526-20034G>A		intron_variant
TSNAX-DISC1	NR_028394.1	n.654-20034G>A		intron_variant
TSNAX-DISC1	NR_028395.1	n.654-20034G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSNAX-DISC1	ENST00000602956.5	n.495+35355G>A		intron_variant		2		ENSP00000473532.1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68257 AN: 151844 Hom.: 17105 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.449 AC: 68266 AN: 151962 Hom.: 17106 Cov.: 31 AF XY: 0.448 AC XY: 33263 AN XY: 74278

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.492

Alfa AF: 0.527 Hom.: 4451

Bravo AF: 0.424

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1765778; hg19: chr1-231732356;