1-231768532-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018662.3(DISC1):​c.1398+1263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 150,392 control chromosomes in the GnomAD database, including 761 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 0.098 ( 761 hom., cov: 32)

Consequence

DISC1
NM_018662.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.316
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DISC1NM_018662.3 linkuse as main transcriptc.1398+1263C>T intron_variant ENST00000439617.8
TSNAX-DISC1NR_028393.1 linkuse as main transcriptn.2119+1263C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DISC1ENST00000439617.8 linkuse as main transcriptc.1398+1263C>T intron_variant 5 NM_018662.3 A2Q9NRI5-1
ENST00000651424.1 linkuse as main transcriptn.537-170G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0977
AC:
14675
AN:
150274
Hom.:
761
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.105
Gnomad AMI
AF:
0.0439
Gnomad AMR
AF:
0.0554
Gnomad ASJ
AF:
0.121
Gnomad EAS
AF:
0.0247
Gnomad SAS
AF:
0.0705
Gnomad FIN
AF:
0.0807
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.112
Gnomad OTH
AF:
0.106
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0977
AC:
14689
AN:
150392
Hom.:
761
Cov.:
32
AF XY:
0.0929
AC XY:
6816
AN XY:
73388
show subpopulations
Gnomad4 AFR
AF:
0.105
Gnomad4 AMR
AF:
0.0554
Gnomad4 ASJ
AF:
0.121
Gnomad4 EAS
AF:
0.0251
Gnomad4 SAS
AF:
0.0710
Gnomad4 FIN
AF:
0.0807
Gnomad4 NFE
AF:
0.112
Gnomad4 OTH
AF:
0.105
Alfa
AF:
0.113
Hom.:
115
Bravo
AF:
0.0947
Asia WGS
AF:
0.0480
AC:
169
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
5.9
DANN
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2793101; hg19: chr1-231904278; API