chr1-11501635-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020780.2(DISP3):c.643G>T(p.Ala215Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00054 in 1,608,942 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0027 ( 2 hom., cov: 34)
Exomes 𝑓: 0.00031 ( 3 hom. )
Consequence
DISP3
NM_020780.2 missense
NM_020780.2 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 0.774
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0053200424).
BP6
?
Variant 1-11501635-G-T is Benign according to our data. Variant chr1-11501635-G-T is described in ClinVar as [Benign]. Clinvar id is 725514.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DISP3 | NM_020780.2 | c.643G>T | p.Ala215Ser | missense_variant | 2/21 | ENST00000294484.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISP3 | ENST00000294484.7 | c.643G>T | p.Ala215Ser | missense_variant | 2/21 | 1 | NM_020780.2 | P1 | |
ENST00000649975.1 | n.382C>A | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.00271 AC: 412AN: 152238Hom.: 2 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000599 AC: 141AN: 235476Hom.: 0 AF XY: 0.000517 AC XY: 67AN XY: 129480
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GnomAD4 exome AF: 0.000312 AC: 455AN: 1456586Hom.: 3 Cov.: 36 AF XY: 0.000293 AC XY: 212AN XY: 724066
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GnomAD4 genome ? AF: 0.00272 AC: 414AN: 152356Hom.: 2 Cov.: 34 AF XY: 0.00260 AC XY: 194AN XY: 74500
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at