13-33523513-C-T

Variant names:

• chr13-33523513-C-T
• rs4943116
• NM_001243476.3:c.30+725G>A

Variant summary

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

The NM_001243476.3(STARD13):​c.30+725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,914 control chromosomes in the GnomAD database, including 14,071 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 0.42 (14071 hom., cov: 32)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD13	NM_001243476.3		c.30+725G>A		intron	N/A	NP_001230405.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230490	ENST00000730896.1		n.1003G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000230490	ENST00000730897.1		n.1133G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000230490	ENST00000437698.1	TSL:3	n.85+725G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64442 AN: 151796 Hom.: 14063 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.424 AC: 64484 AN: 151914 Hom.: 14071 Cov.: 32 AF XY: 0.421 AC XY: 31252 AN XY: 74246

African (AFR) AF: 0.324 AC: 13441 AN: 41456

American (AMR) AF: 0.437 AC: 6661 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2171 AN: 5160

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4239 AN: 10548

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32902 AN: 67914

Other (OTH) AF: 0.448 AC: 944 AN: 2108

Alfa AF: 0.469 Hom.: 27980

Bravo AF: 0.421

Asia WGS AF: 0.458 AC: 1589 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.60
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs4943116; hg19: chr13-34097650;