Variant rs8030587 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_020759.3(STARD9):c.8030G>A(p.Arg2677His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,537,068 control chromosomes in the GnomAD database, including 64,581 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.39 ( 17536 hom., cov: 32)

Exomes 𝑓: 0.23 ( 47045 hom. )

Consequence

STARD9
NM_020759.3 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.77

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]

STARD9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.2557972E-6).

BP6

Variant 15-42689608-G-A is Benign according to our data. Variant chr15-42689608-G-A is described in ClinVar as [Benign]. Clinvar id is 3059971.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD9	NM_020759.3 link	c.8030G>A	p.Arg2677His	missense_variant	23/33	ENST00000290607.12	NP_065810.2	Q9P2P6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD9	ENST00000290607.12 link	c.8030G>A	p.Arg2677His	missense_variant	23/33	5	NM_020759.3	ENSP00000290607.7		Q9P2P6-1
STARD9	ENST00000562619.1 link	n.14G>A		non_coding_transcript_exon_variant	1/10	1		ENSP00000454648.1		H3BN21

Frequencies

GnomAD3 genomes

AF:

0.388

AC:

58933

AN:

151968

Hom.:

17478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.833

Gnomad AMI

AF:

0.0923

Gnomad AMR

AF:

0.199

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.335

GnomAD3 exomes

AF:

0.274

AC:

39065

AN:

142636

Hom.:

7421

AF XY:

0.283

AC XY:

21576

AN XY:

76134

show subpopulations

Gnomad AFR exome

AF:

0.848

Gnomad AMR exome

AF:

0.128

Gnomad ASJ exome

AF:

0.306

Gnomad EAS exome

AF:

0.247

Gnomad SAS exome

AF:

0.436

Gnomad FIN exome

AF:

0.236

Gnomad NFE exome

AF:

0.201

Gnomad OTH exome

AF:

0.248

GnomAD4 exome

AF:

0.233

AC:

322344

AN:

1384982

Hom.:

47045

Cov.:

AF XY:

0.238

AC XY:

162620

AN XY:

683430

show subpopulations

Gnomad4 AFR exome

AF:

0.860

Gnomad4 AMR exome

AF:

0.141

Gnomad4 ASJ exome

AF:

0.305

Gnomad4 EAS exome

AF:

0.225

Gnomad4 SAS exome

AF:

0.438

Gnomad4 FIN exome

AF:

0.240

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.274

GnomAD4 genome

AF:

0.388

AC:

59048

AN:

152086

Hom.:

17536

Cov.:

AF XY:

0.385

AC XY:

28616

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.834

Gnomad4 AMR

AF:

0.199

Gnomad4 ASJ

AF:

0.309

Gnomad4 EAS

AF:

0.230

Gnomad4 SAS

AF:

0.426

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.332

Alfa

AF:

0.232

Hom.:

11746

Bravo

AF:

0.399

TwinsUK

AF:

0.192

AC:

713

ALSPAC

AF:

0.195

AC:

750

ESP6500AA

AF:

0.827

AC:

1144

ESP6500EA

AF:

0.203

AC:

647

ExAC

AF:

0.347

AC:

8107

Asia WGS

AF:

0.351

AC:

1221

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

STARD9-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This 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

AlphaMissense

Benign

0.061

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.018

DANN

Benign

0.11

DEOGEN2

Benign

0.0022

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.00044

LIST_S2

Benign

0.32

MetaRNN

Benign

0.0000013

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.7

PrimateAI

Benign

0.29

PROVEAN

Benign

1.9

REVEL

Benign

0.041

Sift

Benign

1.0

Vest4

0.012

ClinPred

0.0075

GERP RS

-6.4

Varity_R

0.024

gMVP

0.053

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over