chr11-90285120-A-C

Variant summary

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

The ENST00000561596.5(DISC1FP1):​n.33+33803A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,012 control chromosomes in the GnomAD database, including 14,030 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 0.41 ( 14030 hom., cov: 32)

Consequence

DISC1FP1
ENST00000561596.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

Publications

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

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=-0.74).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DISC1FP1NR_104190.1 linkn.86+33803A>C intron_variant Intron 1 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DISC1FP1ENST00000561596.5 linkn.33+33803A>C intron_variant Intron 1 of 6 5
DISC1FP1ENST00000562245.6 linkn.86+33803A>C intron_variant Intron 1 of 6 3
DISC1FP1ENST00000649150.1 linkn.114+33803A>C intron_variant Intron 1 of 7
DISC1FP1ENST00000745652.1 linkn.114+33803A>C intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.409
AC:
62078
AN:
151894
Hom.:
14024
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.215
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.397
Gnomad ASJ
AF:
0.435
Gnomad EAS
AF:
0.387
Gnomad SAS
AF:
0.388
Gnomad FIN
AF:
0.514
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.514
Gnomad OTH
AF:
0.403
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.409
AC:
62111
AN:
152012
Hom.:
14030
Cov.:
32
AF XY:
0.407
AC XY:
30228
AN XY:
74310
show subpopulations
African (AFR)
AF:
0.215
AC:
8922
AN:
41476
American (AMR)
AF:
0.397
AC:
6062
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.435
AC:
1511
AN:
3470
East Asian (EAS)
AF:
0.387
AC:
1998
AN:
5162
South Asian (SAS)
AF:
0.389
AC:
1876
AN:
4818
European-Finnish (FIN)
AF:
0.514
AC:
5425
AN:
10550
Middle Eastern (MID)
AF:
0.374
AC:
110
AN:
294
European-Non Finnish (NFE)
AF:
0.514
AC:
34936
AN:
67940
Other (OTH)
AF:
0.402
AC:
848
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1770
3539
5309
7078
8848
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
578
1156
1734
2312
2890
<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:
0.478
Hom.:
26128
Bravo
AF:
0.394
Asia WGS
AF:
0.360
AC:
1249
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
7.5
DANN
Benign
0.93
PhyloP100
1.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs12364205; hg19: chr11-90018288; API