dbSNP rs3199486: STARD9:n.*1614T>C (chr15-42719997-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000562619.1(STARD9):n.*1614T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 165,114 control chromosomes in the GnomAD database, including 18,741 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 0.40 ( 18202 hom., cov: 32)

Exomes 𝑓: 0.26 ( 539 hom. )

Consequence

STARD9
ENST00000562619.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.120

Publications

5 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD9	NM_020759.3 link	c.*423T>C		3_prime_UTR_variant	Exon 33 of 33	ENST00000290607.12	NP_065810.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
STARD9	ENST00000562619.1 link	n.*1614T>C	non_coding_transcript_exon_variant	Exon 10 of 10	1		ENSP00000454648.1
STARD9	ENST00000290607.12 link	c.*423T>C	3_prime_UTR_variant	Exon 33 of 33	5	NM_020759.3	ENSP00000290607.7
STARD9	ENST00000562619.1 link	n.*1614T>C	3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000454648.1

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61128

AN:

152038

Hom.:

18142

Cov.:

show subpopulations

Gnomad AFR

AF:

0.839

Gnomad AMI

AF:

0.0934

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.246

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.249

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.352

GnomAD4 exome

AF:

0.260

AC:

3369

AN:

12958

Hom.:

539

Cov.:

AF XY:

0.264

AC XY:

1719

AN XY:

6510

show subpopulations

African (AFR)

AF:

0.835

AC:

319

AN:

382

American (AMR)

AF:

0.185

AC:

185

AN:

1000

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

150

AN:

422

East Asian (EAS)

AF:

0.228

AC:

AN:

412

South Asian (SAS)

AF:

0.400

AC:

284

AN:

710

European-Finnish (FIN)

AF:

0.245

AC:

118

AN:

482

Middle Eastern (MID)

AF:

0.352

AC:

AN:

European-Non Finnish (NFE)

AF:

0.227

AC:

1967

AN:

8676

Other (OTH)

AF:

0.284

AC:

233

AN:

820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

119

239

358

478

597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<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:

0.403

AC:

61244

AN:

152156

Hom.:

18202

Cov.:

AF XY:

0.399

AC XY:

29683

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.840

AC:

34848

AN:

41506

American (AMR)

AF:

0.219

AC:

3349

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

1145

AN:

3472

East Asian (EAS)

AF:

0.247

AC:

1277

AN:

5180

South Asian (SAS)

AF:

0.423

AC:

2041

AN:

4824

European-Finnish (FIN)

AF:

0.249

AC:

2635

AN:

10590

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.221

AC:

15046

AN:

67982

Other (OTH)

AF:

0.348

AC:

734

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1285

2570

3856

5141

6426

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

514

1028

1542

2056

2570

<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:

0.261

Hom.:

16325

Bravo

AF:

0.415

Asia WGS

AF:

0.355

AC:

1236

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

-0.12

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

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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