rs3737597

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018662.3(DISC1):​c.*261G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 277,472 control chromosomes in the GnomAD database, including 427 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 0.033 ( 152 hom., cov: 32)
Exomes 𝑓: 0.044 ( 275 hom. )

Consequence

DISC1
NM_018662.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0220
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]
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DISC1NM_018662.3 linkc.*261G>A 3_prime_UTR_variant Exon 13 of 13 ENST00000439617.8 NP_061132.2 Q9NRI5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DISC1ENST00000439617.8 linkc.*261G>A 3_prime_UTR_variant Exon 13 of 13 5 NM_018662.3 ENSP00000403888.4 Q9NRI5-1
DISC1ENST00000366637.8 linkc.*261G>A 3_prime_UTR_variant Exon 13 of 13 5 ENSP00000355597.6 Q9NRI5-2
DISC1ENST00000622252.4 linkc.*1367G>A 3_prime_UTR_variant Exon 12 of 12 5 ENSP00000481791.1 C4P0A0

Frequencies

GnomAD3 genomes
AF:
0.0329
AC:
5002
AN:
152002
Hom.:
151
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0176
Gnomad AMI
AF:
0.0592
Gnomad AMR
AF:
0.0576
Gnomad ASJ
AF:
0.0513
Gnomad EAS
AF:
0.156
Gnomad SAS
AF:
0.0382
Gnomad FIN
AF:
0.0189
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.0276
Gnomad OTH
AF:
0.0432
GnomAD4 exome
AF:
0.0439
AC:
5500
AN:
125352
Hom.:
275
Cov.:
3
AF XY:
0.0424
AC XY:
2691
AN XY:
63536
show subpopulations
Gnomad4 AFR exome
AF:
0.0192
AC:
82
AN:
4266
Gnomad4 AMR exome
AF:
0.0570
AC:
205
AN:
3594
Gnomad4 ASJ exome
AF:
0.0557
AC:
277
AN:
4972
Gnomad4 EAS exome
AF:
0.191
AC:
1995
AN:
10452
Gnomad4 SAS exome
AF:
0.0338
AC:
44
AN:
1300
Gnomad4 FIN exome
AF:
0.0230
AC:
208
AN:
9026
Gnomad4 NFE exome
AF:
0.0281
AC:
2316
AN:
82478
Gnomad4 Remaining exome
AF:
0.0411
AC:
353
AN:
8588
Heterozygous variant carriers
0
246
492
739
985
1231
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
34
68
102
136
170
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0329
AC:
5010
AN:
152120
Hom.:
152
Cov.:
32
AF XY:
0.0331
AC XY:
2463
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.0177
AC:
0.0176652
AN:
0.0176652
Gnomad4 AMR
AF:
0.0576
AC:
0.057642
AN:
0.057642
Gnomad4 ASJ
AF:
0.0513
AC:
0.0513264
AN:
0.0513264
Gnomad4 EAS
AF:
0.156
AC:
0.156419
AN:
0.156419
Gnomad4 SAS
AF:
0.0383
AC:
0.0382696
AN:
0.0382696
Gnomad4 FIN
AF:
0.0189
AC:
0.0189036
AN:
0.0189036
Gnomad4 NFE
AF:
0.0276
AC:
0.0275719
AN:
0.0275719
Gnomad4 OTH
AF:
0.0433
AC:
0.043251
AN:
0.043251
Heterozygous variant carriers
0
244
488
731
975
1219
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
64
128
192
256
320
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0311
Hom.:
436
Bravo
AF:
0.0355
Asia WGS
AF:
0.0790
AC:
276
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.6
DANN
Benign
0.39
Mutation Taster
=100/0
polymorphism (auto)

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: rs3737597; hg19: chr1-232172838; API