rs1489673164
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152326.4(ANKRD9):c.758G>T(p.Gly253Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G253D) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ANKRD9
NM_152326.4 missense
NM_152326.4 missense
Scores
2
5
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.50
Genes affected
ANKRD9 (HGNC:20096): (ankyrin repeat domain 9) Enables ubiquitin ligase-substrate adaptor activity. Involved in cellular copper ion homeostasis; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein ubiquitination. Located in cytoplasmic vesicle and cytosol. Part of Cul5-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ANKRD9 | NM_152326.4 | c.758G>T | p.Gly253Val | missense_variant | Exon 4 of 4 | ENST00000286918.9 | NP_689539.1 | |
| ANKRD9 | NM_001348651.2 | c.758G>T | p.Gly253Val | missense_variant | Exon 4 of 4 | NP_001335580.1 | ||
| ANKRD9 | NM_001348652.2 | c.758G>T | p.Gly253Val | missense_variant | Exon 3 of 3 | NP_001335581.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ANKRD9 | ENST00000286918.9 | c.758G>T | p.Gly253Val | missense_variant | Exon 4 of 4 | 1 | NM_152326.4 | ENSP00000286918.4 | ||
| ANKRD9 | ENST00000559651.1 | c.758G>T | p.Gly253Val | missense_variant | Exon 2 of 2 | 1 | ENSP00000454100.1 | |||
| ANKRD9 | ENST00000560748.5 | c.758G>T | p.Gly253Val | missense_variant | Exon 3 of 3 | 2 | ENSP00000453650.1 | |||
| ANKRD9 | ENST00000559404.5 | c.758G>T | p.Gly253Val | missense_variant | Exon 3 of 3 | 2 | ENSP00000453417.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1321848Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 649822
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1321848
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
649822
Gnomad4 AFR exome
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Gnomad4 AMR exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;.;T;T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;.
Polyphen
P;P;P;.
Vest4
MutPred
Loss of disorder (P = 0.0402);Loss of disorder (P = 0.0402);Loss of disorder (P = 0.0402);Loss of disorder (P = 0.0402);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at