13-33649608-G-A

Variant names:

• chr13-33649608-G-A
• rs9569991
• NM_001243476.3:c.-106+11669C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001243476.3(STARD13):​c.-106+11669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,118 control chromosomes in the GnomAD database, including 1,667 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 0.10 (1667 hom., cov: 31)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 3 publications found

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)

ENSG00000230490 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001243476.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD13	NM_001243476.3		c.-106+11669C>T		intron	N/A	NP_001230405.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230490	ENST00000454681.2	TSL:5	n.91+27070C>T		intron	N/A
	ENSG00000230490	ENST00000653421.2		n.144-14609C>T		intron	N/A
	ENSG00000230490	ENST00000654283.1		n.569+7204C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0999 AC: 15180 AN: 151998 Hom.: 1661 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.100 AC: 15222 AN: 152118 Hom.: 1667 Cov.: 31 AF XY: 0.101 AC XY: 7538 AN XY: 74376

African (AFR) AF: 0.231 AC: 9588 AN: 41440

American (AMR) AF: 0.199 AC: 3045 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00721 AC: 25 AN: 3468

East Asian (EAS) AF: 0.183 AC: 948 AN: 5174

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4824

European-Finnish (FIN) AF: 0.0437 AC: 463 AN: 10596

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 865 AN: 68010

Other (OTH) AF: 0.0931 AC: 197 AN: 2116

Alfa AF: 0.0436 Hom.: 1093

Bravo AF: 0.123

Asia WGS AF: 0.118 AC: 408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		-0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9569991; hg19: chr13-34223745;