rs2038636

Variant summary

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

The NM_018662.3(DISC1):​c.1982-39325G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,006 control chromosomes in the GnomAD database, including 21,129 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 0.52 ( 21129 hom., cov: 32)

Consequence

DISC1
NM_018662.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.549
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DISC1NM_018662.3 linkuse as main transcriptc.1982-39325G>A intron_variant ENST00000439617.8
TSNAX-DISC1NR_028393.1 linkuse as main transcriptn.2648-39325G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DISC1ENST00000439617.8 linkuse as main transcriptc.1982-39325G>A intron_variant 5 NM_018662.3 A2Q9NRI5-1

Frequencies

GnomAD3 genomes
AF:
0.518
AC:
78611
AN:
151888
Hom.:
21128
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.422
Gnomad AMI
AF:
0.654
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.505
Gnomad EAS
AF:
0.208
Gnomad SAS
AF:
0.435
Gnomad FIN
AF:
0.617
Gnomad MID
AF:
0.402
Gnomad NFE
AF:
0.587
Gnomad OTH
AF:
0.510
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.517
AC:
78626
AN:
152006
Hom.:
21129
Cov.:
32
AF XY:
0.513
AC XY:
38100
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.421
Gnomad4 AMR
AF:
0.529
Gnomad4 ASJ
AF:
0.505
Gnomad4 EAS
AF:
0.207
Gnomad4 SAS
AF:
0.436
Gnomad4 FIN
AF:
0.617
Gnomad4 NFE
AF:
0.587
Gnomad4 OTH
AF:
0.506
Alfa
AF:
0.562
Hom.:
17826
Bravo
AF:
0.507
Asia WGS
AF:
0.321
AC:
1117
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
3.0
DANN
Benign
0.65

Splicing

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: rs2038636; hg19: chr1-232055249; API