chr1-231614895-C-T

Variant names:

• chr1-231614895-C-T
• rs1025526
• ENST00000602956.5:n.495+53640C>T

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+53640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,120 control chromosomes in the GnomAD database, including 24,208 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 0.54 (24208 hom., cov: 33)
• Consequence: TSNAX-DISC1 ENST00000602956.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSNAX-DISC1	NR_028393.1		n.526-1749C>T		intron	N/A
	TSNAX-DISC1	NR_028394.1		n.654-1749C>T		intron	N/A
	TSNAX-DISC1	NR_028395.1		n.654-1749C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSNAX-DISC1	ENST00000602956.5	TSL:2	n.495+53640C>T		intron	N/A	ENSP00000473532.1	C4P0D8
	TSNAX-DISC1	ENST00000602567.1	TSL:2	n.496-1749C>T		intron	N/A	ENSP00000473456.1	C4P0D6
	TSNAX-DISC1	ENST00000602634.5	TSL:2	n.368-1749C>T		intron	N/A	ENSP00000473307.1	C4P0D4

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82749 AN: 152002 Hom.: 24199 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.544 AC: 82777 AN: 152120 Hom.: 24208 Cov.: 33 AF XY: 0.540 AC XY: 40130 AN XY: 74352

African (AFR) AF: 0.359 AC: 14901 AN: 41466

American (AMR) AF: 0.522 AC: 7982 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3470

East Asian (EAS) AF: 0.186 AC: 962 AN: 5178

South Asian (SAS) AF: 0.576 AC: 2780 AN: 4830

European-Finnish (FIN) AF: 0.624 AC: 6593 AN: 10564

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.665 AC: 45242 AN: 68008

Other (OTH) AF: 0.584 AC: 1230 AN: 2106

Alfa AF: 0.600 Hom.: 3517

Bravo AF: 0.525

Asia WGS AF: 0.413 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.58
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1025526; hg19: chr1-231750641; COSMIC: COSV71449416;