13-33469613-C-T

Variant names:

• chr13-33469613-C-T
• rs9315215
• NM_001243476.3:c.31-29889G>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.31-29889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,782 control chromosomes in the GnomAD database, including 8,049 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 0.31 (8049 hom., cov: 32)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.31-29889G>A		intron_variant	Intron 4 of 17		NP_001230405.1
STARD13	XM_047430759.1	c.166-29889G>A		intron_variant	Intron 2 of 15		XP_047286715.1
STARD13	XM_017020835.3	c.31-29889G>A		intron_variant	Intron 2 of 15		XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000454681.2	n.227-29889G>A		intron_variant	Intron 2 of 5	5
ENSG00000230490	ENST00000686875.1	n.279-29889G>A		intron_variant	Intron 2 of 3
ENSG00000230490	ENST00000730869.1	n.630-29889G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47571 AN: 151664 Hom.: 8048 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.313 AC: 47582 AN: 151782 Hom.: 8049 Cov.: 32 AF XY: 0.308 AC XY: 22861 AN XY: 74150

African (AFR) AF: 0.187 AC: 7719 AN: 41356

American (AMR) AF: 0.333 AC: 5082 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1126 AN: 5150

South Asian (SAS) AF: 0.327 AC: 1573 AN: 4812

European-Finnish (FIN) AF: 0.312 AC: 3283 AN: 10524

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26468 AN: 67922

Other (OTH) AF: 0.331 AC: 697 AN: 2104

Alfa AF: 0.363 Hom.: 31492

Bravo AF: 0.310

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs9315215; hg19: chr13-34043750;