chr11-90639135-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000561596.5(DISC1FP1):​n.279+36227G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

DISC1FP1
ENST00000561596.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.181

Publications

5 publications found
Variant links:
Genes affected
DISC1FP1 (HGNC:33625): (DISC1 fusion partner 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DISC1FP1NR_104190.1 linkn.332+36227G>T intron_variant Intron 3 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DISC1FP1ENST00000561596.5 linkn.279+36227G>T intron_variant Intron 3 of 6 5
DISC1FP1ENST00000562245.6 linkn.332+36227G>T intron_variant Intron 3 of 6 3
DISC1FP1ENST00000562678.5 linkn.185+92240G>T intron_variant Intron 2 of 5 3

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.73
DANN
Benign
0.28
PhyloP100
0.18

Splicing

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

Publications

Other links and lift over

dbSNP: rs660753; hg19: chr11-90372303; API