1-231878664-G-T

Position:

• chr1-231878664-G-T

Variant summary

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

The NM_018662.3(DISC1):​c.1981+60147G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,886 control chromosomes in the GnomAD database, including 8,960 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 0.34 (8960 hom., cov: 31)
• Consequence: DISC1 NM_018662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

DISC1 (HGNC:2888): (DISC1 scaffold protein) This gene encodes a protein with multiple coiled coil motifs which is located in the nucleus, cytoplasm and mitochondria. The protein is involved in neurite outgrowth and cortical development through its interaction with other proteins. This gene is disrupted in a t(1;11)(q42.1;q14.3) translocation which segregates with schizophrenia and related psychiatric disorders in a large Scottish family. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

TSNAX-DISC1 (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 = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DISC1	NM_018662.3	c.1981+60147G>T		intron_variant		ENST00000439617.8
TSNAX-DISC1	NR_028393.1	n.2647+60147G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DISC1	ENST00000439617.8	c.1981+60147G>T		intron_variant		5	NM_018662.3	A2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51674 AN: 151766 Hom.: 8963 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.340 AC: 51687 AN: 151886 Hom.: 8960 Cov.: 31 AF XY: 0.341 AC XY: 25273 AN XY: 74196

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.342

Alfa AF: 0.352 Hom.: 1156

Bravo AF: 0.335

Asia WGS AF: 0.234 AC: 812 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	0.049
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7535913; hg19: chr1-232014410;