rs3806372

Variant names:

• chr1-231626398-C-A
• rs3806372
• ENST00000602956.5:n.495+65143C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-231626398-C-A
• chr1-231626398-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000602956.5(TSNAX-DISC1):​n.495+65143C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 148,118 control chromosomes in the GnomAD database, including 52 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 0.021 (52 hom., cov: 30)
• Consequence: TSNAX-DISC1 ENST00000602956.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 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=-0.8).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0213 (3160/148118) while in subpopulation AMR AF = 0.0462 (691/14942). AF 95% confidence interval is 0.0434. There are 52 homozygotes in GnomAd4. There are 1564 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSNAX-DISC1	NR_028393.1	n.788+9492C>A		intron_variant	Intron 5 of 15
TSNAX-DISC1	NR_028394.1	n.916+9492C>A		intron_variant	Intron 6 of 13
TSNAX-DISC1	NR_028395.1	n.916+9492C>A		intron_variant	Intron 6 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSNAX-DISC1	ENST00000602956.5	n.495+65143C>A		intron_variant	Intron 5 of 12	2		ENSP00000473532.1

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 3161 AN: 148008 Hom.: 52 Cov.: 30

Gnomad AFR AF: 0.00630

Gnomad AMI AF: 0.0156

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.00854

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0275

Gnomad OTH AF: 0.0121

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

GnomAD4 genome AF: 0.0213 AC: 3160 AN: 148118 Hom.: 52 Cov.: 30 AF XY: 0.0216 AC XY: 1564 AN XY: 72270

African (AFR) AF: 0.00628 AC: 255 AN: 40576

American (AMR) AF: 0.0462 AC: 691 AN: 14942

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3442

East Asian (EAS) AF: 0.00231 AC: 11 AN: 4752

South Asian (SAS) AF: 0.00855 AC: 38 AN: 4446

European-Finnish (FIN) AF: 0.0257 AC: 252 AN: 9822

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0275 AC: 1837 AN: 66862

Other (OTH) AF: 0.0120 AC: 25 AN: 2082

Alfa AF: 0.0151 Hom.: 13

Bravo AF: 0.0218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.15
DANN	Benign	0.43
PhyloP100		-1.5
PromoterAI		-0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3806372; hg19: chr1-231762144;