Genetic Variant STARD13:c.3225-197A>G (chr13-33105907-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 NM_178006.4(STARD13):c.3225-197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,170 control chromosomes in the GnomAD database, including 37,757 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 0.70 ( 37757 hom., cov: 33)

Consequence

STARD13
NM_178006.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.627

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:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178006.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
STARD13	NM_178006.4	MANE Select	c.3225-197A>G	intron	N/A	NP_821074.1
STARD13	NM_178007.3		c.3201-197A>G	intron	N/A	NP_821075.1
STARD13	NM_001411014.1		c.3180-197A>G	intron	N/A	NP_001397943.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
STARD13	ENST00000336934.10	TSL:1 MANE Select	c.3225-197A>G	intron	N/A	ENSP00000338785.4
STARD13	ENST00000255486.8	TSL:1	c.3201-197A>G	intron	N/A	ENSP00000255486.4
STARD13	ENST00000567873.2	TSL:1	c.3180-197A>G	intron	N/A	ENSP00000456233.2

Frequencies

GnomAD3 genomes

AF:

0.700

AC:

106471

AN:

152052

Hom.:

37710

Cov.:

show subpopulations

Gnomad AFR

AF:

0.803

Gnomad AMI

AF:

0.766

Gnomad AMR

AF:

0.636

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.699

Gnomad FIN

AF:

0.679

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.667

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.700

AC:

106574

AN:

152170

Hom.:

37757

Cov.:

AF XY:

0.700

AC XY:

52054

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.803

AC:

33329

AN:

41520

American (AMR)

AF:

0.636

AC:

9724

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.595

AC:

2065

AN:

3468

East Asian (EAS)

AF:

0.754

AC:

3896

AN:

5170

South Asian (SAS)

AF:

0.697

AC:

3366

AN:

4828

European-Finnish (FIN)

AF:

0.679

AC:

7182

AN:

10584

Middle Eastern (MID)

AF:

0.663

AC:

195

AN:

294

European-Non Finnish (NFE)

AF:

0.657

AC:

44701

AN:

67994

Other (OTH)

AF:

0.670

AC:

1417

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1673

3346

5019

6692

8365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<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:

0.673

Hom.:

48441

Bravo

AF:

0.700

Asia WGS

AF:

0.736

AC:

2559

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.3

(source)

DANN

Benign

0.31

PhyloP100

-0.63

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over