rs11122324
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000317586.8(DISC1):c.*834G>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 0.354 in 985,294 control chromosomes in the GnomAD database, including 62,125 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 0.36 ( 10182 hom., cov: 32)
Exomes 𝑓: 0.35 ( 51943 hom. )
Consequence
DISC1
ENST00000317586.8 3_prime_UTR
ENST00000317586.8 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.197
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DISC1 | NM_018662.3 | c.1117+21411G>A | intron_variant | ENST00000439617.8 | |||
TSNAX-DISC1 | NR_028393.1 | n.1838+21411G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISC1 | ENST00000439617.8 | c.1117+21411G>A | intron_variant | 5 | NM_018662.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.364 AC: 55231AN: 151922Hom.: 10168 Cov.: 32
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GnomAD4 exome AF: 0.353 AC: 293786AN: 833252Hom.: 51943 Cov.: 31 AF XY: 0.352 AC XY: 135580AN XY: 384796
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GnomAD4 genome ? AF: 0.364 AC: 55282AN: 152042Hom.: 10182 Cov.: 32 AF XY: 0.357 AC XY: 26554AN XY: 74316
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at