Genetic Variant ENST00000487412.5:n.720C>T (chr13-33138648-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000487412.5(STARD13):n.720C>T 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 0.0875 in 271,552 control chromosomes in the GnomAD database, including 1,298 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 0.095 ( 830 hom., cov: 32)

Exomes 𝑓: 0.078 ( 468 hom. )

Consequence

STARD13
ENST00000487412.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.380

Publications

2 publications found

Variant links:

Genes affected

STARD13 (HGNC:19164): (StAR related lipid transfer domain containing 13) This gene encodes a protein which contains an N-terminal sterile alpha motif (SAM) for protein-protein interactions, followed by an ATP/GTP-binding motif, a GTPase-activating protein (GAP) domain, and a C-terminal STAR-related lipid transfer (START) domain. It may be involved in regulation of cytoskeletal reorganization, cell proliferation, and cell motility, and acts as a tumor suppressor in hepatoma cells. The gene is located in a region of chromosome 13 that is associated with loss of heterozygosity in hepatocellular carcinomas. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

STARD13 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

STARD13 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_178006.4 link	c.387+3662C>T		intron_variant	Intron 4 of 13	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10 link	c.387+3662C>T		intron_variant	Intron 4 of 13	1	NM_178006.4	ENSP00000338785.4

Frequencies

GnomAD3 genomes

AF:

0.0946

AC:

14392

AN:

152076

Hom.:

829

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.0713

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0758

Gnomad EAS

AF:

0.246

Gnomad SAS

AF:

0.0957

Gnomad FIN

AF:

0.0943

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0650

Gnomad OTH

AF:

0.105

GnomAD4 exome

AF:

0.0783

AC:

9344

AN:

119358

Hom.:

468

Cov.:

AF XY:

0.0808

AC XY:

5246

AN XY:

64956

show subpopulations

African (AFR)

AF:

0.102

AC:

234

AN:

2288

American (AMR)

AF:

0.125

AC:

504

AN:

4030

Ashkenazi Jewish (ASJ)

AF:

0.0699

AC:

195

AN:

2788

East Asian (EAS)

AF:

0.226

AC:

721

AN:

3188

South Asian (SAS)

AF:

0.0954

AC:

2314

AN:

24250

European-Finnish (FIN)

AF:

0.0938

AC:

720

AN:

7676

Middle Eastern (MID)

AF:

0.0648

AC:

AN:

432

European-Non Finnish (NFE)

AF:

0.0608

AC:

4171

AN:

68596

Other (OTH)

AF:

0.0748

AC:

457

AN:

6110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

395

790

1186

1581

1976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

138

184

230

<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:

0.0947

AC:

14414

AN:

152194

Hom.:

830

Cov.:

AF XY:

0.0963

AC XY:

7168

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.115

AC:

4781

AN:

41532

American (AMR)

AF:

0.126

AC:

1922

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0758

AC:

263

AN:

3470

East Asian (EAS)

AF:

0.246

AC:

1267

AN:

5156

South Asian (SAS)

AF:

0.0956

AC:

461

AN:

4822

European-Finnish (FIN)

AF:

0.0943

AC:

1000

AN:

10602

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0650

AC:

4423

AN:

68008

Other (OTH)

AF:

0.105

AC:

222

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

652

1305

1957

2610

3262

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<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:

0.0788

Hom.:

1457

Bravo

AF:

0.102

Asia WGS

AF:

0.161

AC:

559

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.9

(source)

DANN

Benign

0.86

PhyloP100

0.38

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