rs1765778

Variant names:

• chr1-231596610-G-A
• rs1765778
• ENST00000602956.5:n.495+35355G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602956.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSNAX-DISC1	NR_028393.1		n.526-20034G>A		intron	N/A
	TSNAX-DISC1	NR_028394.1		n.654-20034G>A		intron	N/A
	TSNAX-DISC1	NR_028395.1		n.654-20034G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSNAX-DISC1	ENST00000602956.5	TSL:2	n.495+35355G>A		intron	N/A	ENSP00000473532.1
	LINC00582	ENST00000448058.2	TSL:2	n.240-4810C>T		intron	N/A
	TSNAX-DISC1	ENST00000602567.1	TSL:2	n.496-20034G>A		intron	N/A	ENSP00000473456.1

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

African (AFR) AF: 0.247 AC: 10225 AN: 41456

American (AMR) AF: 0.400 AC: 6101 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2003 AN: 3468

East Asian (EAS) AF: 0.176 AC: 911 AN: 5170

South Asian (SAS) AF: 0.509 AC: 2454 AN: 4822

European-Finnish (FIN) AF: 0.557 AC: 5879 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38936 AN: 67926

Other (OTH) AF: 0.492 AC: 1038 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.78
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1765778; hg19: chr1-231732356;