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GeneBe

1-11501880-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_020780.2(DISP3):c.888C>T(p.Val296=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 1,612,950 control chromosomes in the GnomAD database, including 10,381 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 2897 hom., cov: 34)
Exomes 𝑓: 0.084 ( 7484 hom. )

Consequence

DISP3
NM_020780.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.534
Variant links:
Genes affected
DISP3 (HGNC:29251): (dispatched RND transporter family member 3) Involved in negative regulation of neuron differentiation; positive regulation of lipid metabolic process; and positive regulation of neural precursor cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-11501880-C-T is Benign according to our data. Variant chr1-11501880-C-T is described in ClinVar as [Benign]. Clinvar id is 3058907.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.534 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DISP3NM_020780.2 linkuse as main transcriptc.888C>T p.Val296= synonymous_variant 2/21 ENST00000294484.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DISP3ENST00000294484.7 linkuse as main transcriptc.888C>T p.Val296= synonymous_variant 2/211 NM_020780.2 P1Q9P2K9-1
ENST00000649975.1 linkuse as main transcriptn.137G>A non_coding_transcript_exon_variant 1/2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.153
AC:
23271
AN:
152138
Hom.:
2892
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.342
Gnomad AMI
AF:
0.0822
Gnomad AMR
AF:
0.0741
Gnomad ASJ
AF:
0.118
Gnomad EAS
AF:
0.0449
Gnomad SAS
AF:
0.199
Gnomad FIN
AF:
0.128
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.0680
Gnomad OTH
AF:
0.125
GnomAD3 exomes
AF:
0.105
AC:
26001
AN:
248284
Hom.:
2222
AF XY:
0.108
AC XY:
14516
AN XY:
134940
show subpopulations
Gnomad AFR exome
AF:
0.350
Gnomad AMR exome
AF:
0.0445
Gnomad ASJ exome
AF:
0.118
Gnomad EAS exome
AF:
0.0384
Gnomad SAS exome
AF:
0.203
Gnomad FIN exome
AF:
0.123
Gnomad NFE exome
AF:
0.0700
Gnomad OTH exome
AF:
0.0813
GnomAD4 exome
AF:
0.0839
AC:
122493
AN:
1460694
Hom.:
7484
Cov.:
37
AF XY:
0.0870
AC XY:
63183
AN XY:
726526
show subpopulations
Gnomad4 AFR exome
AF:
0.349
Gnomad4 AMR exome
AF:
0.0477
Gnomad4 ASJ exome
AF:
0.122
Gnomad4 EAS exome
AF:
0.0406
Gnomad4 SAS exome
AF:
0.199
Gnomad4 FIN exome
AF:
0.119
Gnomad4 NFE exome
AF:
0.0663
Gnomad4 OTH exome
AF:
0.0990
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.153
AC:
23300
AN:
152256
Hom.:
2897
Cov.:
34
AF XY:
0.154
AC XY:
11492
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.342
Gnomad4 AMR
AF:
0.0740
Gnomad4 ASJ
AF:
0.118
Gnomad4 EAS
AF:
0.0448
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.128
Gnomad4 NFE
AF:
0.0680
Gnomad4 OTH
AF:
0.123
Alfa
AF:
0.0815
Hom.:
1545
Bravo
AF:
0.152
Asia WGS
AF:
0.146
AC:
508
AN:
3478
EpiCase
AF:
0.0727
EpiControl
AF:
0.0678

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

DISP3-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 30, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
Cadd
Benign
16
Dann
Benign
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs12144924; hg19: chr1-11561937; API