13-33513466-C-T

Variant names:

• chr13-33513466-C-T
• rs9315220
• NM_001243476.3:c.30+10772G>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+10772G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,092 control chromosomes in the GnomAD database, including 7,466 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 0.30 (7466 hom., cov: 32)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.30+10772G>A		intron_variant	Intron 4 of 17		NP_001230405.1
STARD13	XM_047430759.1	c.165+10772G>A		intron_variant	Intron 2 of 15		XP_047286715.1
STARD13	XM_017020835.3	c.30+10772G>A		intron_variant	Intron 2 of 15		XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000437698.1	n.278-2059G>A		intron_variant	Intron 2 of 2	3
ENSG00000230490	ENST00000454681.2	n.226+10772G>A		intron_variant	Intron 2 of 5	5
ENSG00000230490	ENST00000686875.1	n.278+10772G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45794 AN: 151974 Hom.: 7468 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.301 AC: 45797 AN: 152092 Hom.: 7466 Cov.: 32 AF XY: 0.296 AC XY: 22037 AN XY: 74336

African (AFR) AF: 0.175 AC: 7265 AN: 41522

American (AMR) AF: 0.329 AC: 5028 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1124 AN: 5156

South Asian (SAS) AF: 0.325 AC: 1563 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3085 AN: 10570

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25435 AN: 67974

Other (OTH) AF: 0.326 AC: 688 AN: 2110

Alfa AF: 0.342 Hom.: 4582

Bravo AF: 0.300

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.39
DANN	Benign	0.42
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs9315220; hg19: chr13-34087603;