rs1945521873

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001940.4(ATN1):​c.467C>A​(p.Ala156Asp) variant causes a missense 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. 12/21 in silico tools predict 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: 31)

Consequence

ATN1
NM_001940.4 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.49
Variant links:
Genes affected
ATN1 (HGNC:3033): (atrophin 1) Dentatorubral pallidoluysian atrophy (DRPLA) is a rare neurodegenerative disorder characterized by cerebellar ataxia, myoclonic epilepsy, choreoathetosis, and dementia. The disorder is related to the expansion from 7-35 copies to 49-93 copies of a trinucleotide repeat (CAG/CAA) within this gene. The encoded protein includes a serine repeat and a region of alternating acidic and basic amino acids, as well as the variable glutamine repeat. Alternative splicing results in two transcripts variants that encode the same protein. [provided by RefSeq, Jul 2016]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1647265).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATN1NM_001940.4 linkc.467C>A p.Ala156Asp missense_variant Exon 5 of 10 ENST00000396684.3 NP_001931.2 P54259

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATN1ENST00000396684.3 linkc.467C>A p.Ala156Asp missense_variant Exon 5 of 10 1 NM_001940.4 ENSP00000379915.2 P54259
ATN1ENST00000356654.8 linkc.467C>A p.Ala156Asp missense_variant Exon 5 of 10 1 ENSP00000349076.3 P54259

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
37
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.34
BayesDel_addAF
Benign
-0.021
T
BayesDel_noAF
Benign
-0.27
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.38
T;T
Eigen
Benign
-0.22
Eigen_PC
Benign
-0.098
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Benign
0.74
.;T
M_CAP
Benign
0.043
D
MetaRNN
Benign
0.16
T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
0.34
N;N
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
-1.7
N;N
REVEL
Benign
0.14
Sift
Uncertain
0.0010
D;D
Sift4G
Benign
0.35
T;T
Polyphen
0.41
B;B
Vest4
0.50
MutPred
0.33
Gain of catalytic residue at P161 (P = 5e-04);Gain of catalytic residue at P161 (P = 5e-04);
MVP
0.28
MPC
0.51
ClinPred
0.54
D
GERP RS
3.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.52
gMVP
0.22

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: rs1945521873; hg19: chr12-7044897; API