Genetic Variant STARD9:c.*745A>G (chr15-42720319-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020759.3(STARD9):c.*745A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,290 control chromosomes in the GnomAD database, including 18,184 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 ( 18171 hom., cov: 31)

Exomes 𝑓: 0.26 ( 13 hom. )

Consequence

STARD9
NM_020759.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

Publications

4 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:

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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=-0.94).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020759.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD9	NM_020759.3	MANE Select	c.*745A>G		3_prime_UTR	Exon 33 of 33	NP_065810.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STARD9	ENST00000290607.12	TSL:5 MANE Select	c.*745A>G	3_prime_UTR	Exon 33 of 33	ENSP00000290607.7	Q9P2P6-1
STARD9	ENST00000562619.1	TSL:1	n.*1936A>G	non_coding_transcript_exon	Exon 10 of 10	ENSP00000454648.1	H3BN21
STARD9	ENST00000562619.1	TSL:1	n.*1936A>G	3_prime_UTR	Exon 10 of 10	ENSP00000454648.1	H3BN21

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61062

AN:

151918

Hom.:

18111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.839

Gnomad AMI

AF:

0.0923

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.426

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.352

GnomAD4 exome

AF:

0.256

AC:

AN:

254

Hom.:

Cov.:

AF XY:

0.301

AC XY:

AN XY:

156

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.203

AC:

AN:

128

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.264

AC:

AN:

106

Other (OTH)

AF:

0.300

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.402

AC:

61178

AN:

152036

Hom.:

18171

Cov.:

AF XY:

0.399

AC XY:

29669

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.840

AC:

34810

AN:

41464

American (AMR)

AF:

0.219

AC:

3344

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

1145

AN:

3470

East Asian (EAS)

AF:

0.246

AC:

1271

AN:

5164

South Asian (SAS)

AF:

0.426

AC:

2052

AN:

4820

European-Finnish (FIN)

AF:

0.248

AC:

2624

AN:

10574

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.221

AC:

15029

AN:

67956

Other (OTH)

AF:

0.348

AC:

735

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1260

2519

3779

5038

6298

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:

0.278

Hom.:

10031

Bravo

AF:

0.415

Asia WGS

AF:

0.359

AC:

1248

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.2

(source)

DANN

Benign

0.65

PhyloP100

0.13

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over