1-231567179-G-C

Variant names:

• chr1-231567179-G-C
• rs6662926
• ENST00000602956.5:n.495+5924G>C

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+5924G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,160 control chromosomes in the GnomAD database, including 51,623 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 0.82 (51623 hom., cov: 33)
• Consequence: TSNAX-DISC1 ENST00000602956.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.876 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.525+24568G>C		intron	N/A
	TSNAX-DISC1	NR_028394.1		n.653+5924G>C		intron	N/A
	TSNAX-DISC1	NR_028395.1		n.653+5924G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSNAX-DISC1	ENST00000602956.5	TSL:2	n.495+5924G>C		intron	N/A	ENSP00000473532.1	C4P0D8
	TSNAX-DISC1	ENST00000602567.1	TSL:2	n.495+5924G>C		intron	N/A	ENSP00000473456.1	C4P0D6
	TSNAX-DISC1	ENST00000602634.5	TSL:2	n.367+24568G>C		intron	N/A	ENSP00000473307.1	C4P0D4

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124525 AN: 152042 Hom.: 51592 Cov.: 33

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.819 AC: 124603 AN: 152160 Hom.: 51623 Cov.: 33 AF XY: 0.816 AC XY: 60735 AN XY: 74392

African (AFR) AF: 0.742 AC: 30788 AN: 41478

American (AMR) AF: 0.821 AC: 12555 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3080 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2658 AN: 5150

South Asian (SAS) AF: 0.694 AC: 3352 AN: 4830

European-Finnish (FIN) AF: 0.894 AC: 9474 AN: 10600

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59976 AN: 68024

Other (OTH) AF: 0.813 AC: 1718 AN: 2114

Alfa AF: 0.827 Hom.: 3057

Bravo AF: 0.811

Asia WGS AF: 0.624 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.25
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6662926; hg19: chr1-231702925; COSMIC: COSV107466851;