13-33575251-C-A

Variant names:

• chr13-33575251-C-A
• rs1928393
• NM_001243476.3:c.-105-50879G>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.-105-50879G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,792 control chromosomes in the GnomAD database, including 5,352 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 0.24 (5352 hom., cov: 31)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.-105-50879G>T		intron_variant	Intron 3 of 17		NP_001230405.1
STARD13	XM_017020835.3	c.-105-50879G>T		intron_variant	Intron 1 of 15		XP_016876324.1
LOC102723406	XR_001749811.2	n.250+4408C>A		intron_variant	Intron 2 of 4
LOC102723406	XR_007063750.1	n.353+4408C>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000454681.2	n.92-50879G>T		intron_variant	Intron 1 of 5	5
ENSG00000230490	ENST00000686875.1	n.144-50879G>T		intron_variant	Intron 1 of 3
ENSG00000230490	ENST00000730869.1	n.495-50879G>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36702 AN: 151674 Hom.: 5323 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.242 AC: 36791 AN: 151792 Hom.: 5352 Cov.: 31 AF XY: 0.240 AC XY: 17805 AN XY: 74174

African (AFR) AF: 0.382 AC: 15804 AN: 41376

American (AMR) AF: 0.249 AC: 3794 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2215 AN: 5140

South Asian (SAS) AF: 0.169 AC: 814 AN: 4804

European-Finnish (FIN) AF: 0.141 AC: 1481 AN: 10524

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11312 AN: 67924

Other (OTH) AF: 0.252 AC: 531 AN: 2110

Alfa AF: 0.185 Hom.: 1494

Bravo AF: 0.260

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.064
DANN	Benign	0.61
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1928393; hg19: chr13-34149388;