rs184535522

Variant summary

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

The NM_020759.3(STARD9):​c.206A>C​(p.Glu69Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000144 in 1,384,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. 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. E69G) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

STARD9
NM_020759.3 missense

Scores

5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.73
Variant links:
Genes affected
STARD9 (HGNC:19162): (StAR related lipid transfer domain containing 9) Enables microtubule binding activity and microtubule motor activity. Involved in spindle assembly. Located in centriole; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.22914857).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STARD9NM_020759.3 linkc.206A>C p.Glu69Ala missense_variant Exon 3 of 33 ENST00000290607.12 NP_065810.2 Q9P2P6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STARD9ENST00000290607.12 linkc.206A>C p.Glu69Ala missense_variant Exon 3 of 33 5 NM_020759.3 ENSP00000290607.7 Q9P2P6-1
STARD9ENST00000564158.5 linkn.263A>C non_coding_transcript_exon_variant Exon 3 of 14 1
STARD9ENST00000563872.5 linkn.252A>C non_coding_transcript_exon_variant Exon 3 of 6 4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000144
AC:
2
AN:
1384338
Hom.:
0
Cov.:
30
AF XY:
0.00000146
AC XY:
1
AN XY:
683138
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000185
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.048
T
BayesDel_noAF
Benign
-0.31
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.23
T
Eigen
Benign
0.14
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Uncertain
0.84
D
LIST_S2
Uncertain
0.95
D
M_CAP
Benign
0.019
T
MetaRNN
Benign
0.23
T
MetaSVM
Benign
-0.51
T
MutationAssessor
Benign
0.83
L
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-2.3
N
REVEL
Benign
0.11
Sift
Benign
0.11
T
Vest4
0.46
MutPred
0.40
Loss of disorder (P = 0.0609);
MVP
0.53
ClinPred
0.65
D
GERP RS
4.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.13
gMVP
0.30

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-42877807; API