dbSNP rs16957063: STARD9:p.Thr3504Thr (chr15-42692090-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_020759.3(STARD9):c.10512A>G(p.Thr3504Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 1,537,146 control chromosomes in the GnomAD database, including 1,352 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.058 ( 584 hom., cov: 32)

Exomes 𝑓: 0.017 ( 768 hom. )

Consequence

STARD9
NM_020759.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.249

Publications

15 publications found

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 was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP7

Synonymous conserved (PhyloP=-0.249 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD9	NM_020759.3 link	c.10512A>G	p.Thr3504Thr	synonymous_variant	Exon 23 of 33	ENST00000290607.12	NP_065810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD9	ENST00000290607.12 link	c.10512A>G	p.Thr3504Thr	synonymous_variant	Exon 23 of 33	5	NM_020759.3	ENSP00000290607.7
STARD9	ENST00000562619.1 link	n.2496A>G		non_coding_transcript_exon_variant	Exon 1 of 10	1		ENSP00000454648.1

Frequencies

GnomAD3 genomes

AF:

0.0577

AC:

8776

AN:

152120

Hom.:

582

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0247

Gnomad ASJ

AF:

0.0329

Gnomad EAS

AF:

0.0581

Gnomad SAS

AF:

0.0331

Gnomad FIN

AF:

0.00499

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0426

GnomAD2 exomes

AF:

0.0291

AC:

4044

AN:

139172

AF XY:

0.0286

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.0127

Gnomad ASJ exome

AF:

0.0332

Gnomad EAS exome

AF:

0.0636

Gnomad FIN exome

AF:

0.00297

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.0229

GnomAD4 exome

AF:

0.0168

AC:

23296

AN:

1384908

Hom.:

768

Cov.:

AF XY:

0.0170

AC XY:

11634

AN XY:

683384

show subpopulations

African (AFR)

AF:

0.182

AC:

5764

AN:

31592

American (AMR)

AF:

0.0146

AC:

521

AN:

35700

Ashkenazi Jewish (ASJ)

AF:

0.0356

AC:

896

AN:

25182

East Asian (EAS)

AF:

0.0499

AC:

1782

AN:

35734

South Asian (SAS)

AF:

0.0348

AC:

2754

AN:

79234

European-Finnish (FIN)

AF:

0.00366

AC:

128

AN:

34976

Middle Eastern (MID)

AF:

0.0165

AC:

AN:

5696

European-Non Finnish (NFE)

AF:

0.00918

AC:

9905

AN:

1078882

Other (OTH)

AF:

0.0251

AC:

1452

AN:

57912

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

1454

2907

4361

5814

7268

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

498

996

1494

1992

2490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0578

AC:

8798

AN:

152238

Hom.:

584

Cov.:

AF XY:

0.0564

AC XY:

4201

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.168

AC:

6981

AN:

41510

American (AMR)

AF:

0.0247

AC:

377

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0329

AC:

114

AN:

3470

East Asian (EAS)

AF:

0.0582

AC:

302

AN:

5188

South Asian (SAS)

AF:

0.0333

AC:

161

AN:

4828

European-Finnish (FIN)

AF:

0.00499

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0105

AC:

713

AN:

68020

Other (OTH)

AF:

0.0427

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

391

782

1173

1564

1955

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0291

Hom.:

774

Bravo

AF:

0.0636

Asia WGS

AF:

0.0530

AC:

184

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.71

(source)

DANN

Benign

0.27

PhyloP100

-0.25

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over