rs999708

chr1-231875845-A-Gchr1-231875845-A-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+57328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,946 control chromosomes in the GnomAD database, including 19,124 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 0.50 (19124 hom., cov: 31)
• Consequence: DISC1 NM_018662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DISC1	NM_018662.3	c.1981+57328A>G		intron_variant		ENST00000439617.8
TSNAX-DISC1	NR_028393.1	n.2647+57328A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DISC1	ENST00000439617.8	c.1981+57328A>G		intron_variant		5	NM_018662.3	A2

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75834 AN: 151828 Hom.: 19107 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.499 AC: 75894 AN: 151946 Hom.: 19124 Cov.: 31 AF XY: 0.499 AC XY: 37034 AN XY: 74284

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.494

Alfa AF: 0.323 Hom.: 745

Bravo AF: 0.507

Asia WGS AF: 0.480 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.7
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999708; hg19: chr1-232011591;