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GeneBe

rs1754603

Variant summary

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

The NM_018662.3(DISC1):c.2043-5909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,790 control chromosomes in the GnomAD database, including 6,430 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 0.29 ( 6430 hom., cov: 32)

Consequence

DISC1
NM_018662.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.589
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DISC1NM_018662.3 linkuse as main transcriptc.2043-5909C>T intron_variant ENST00000439617.8
TSNAX-DISC1NR_028393.1 linkuse as main transcriptn.2709-5909C>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.2043-5909C>T intron_variant 5 NM_018662.3 A2Q9NRI5-1

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43246
AN:
151670
Hom.:
6421
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.333
Gnomad AMI
AF:
0.449
Gnomad AMR
AF:
0.182
Gnomad ASJ
AF:
0.247
Gnomad EAS
AF:
0.120
Gnomad SAS
AF:
0.273
Gnomad FIN
AF:
0.329
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.287
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.285
AC:
43288
AN:
151790
Hom.:
6430
Cov.:
32
AF XY:
0.284
AC XY:
21061
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.333
Gnomad4 AMR
AF:
0.181
Gnomad4 ASJ
AF:
0.247
Gnomad4 EAS
AF:
0.119
Gnomad4 SAS
AF:
0.274
Gnomad4 FIN
AF:
0.329
Gnomad4 NFE
AF:
0.287
Gnomad4 OTH
AF:
0.259
Alfa
AF:
0.285
Hom.:
772
Bravo
AF:
0.272
Asia WGS
AF:
0.220
AC:
764
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.65
Dann
Benign
0.27

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: rs1754603; hg19: chr1-232138622; COSMIC: COSV64093789; API