rs1928393

Positions:

• chr13-33575251-C-A
• chr13-33575251-C-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ENSG00000230490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.-105-50879G>T		intron_variant			NP_001230405.1
STARD13	XM_017020835.3	c.-105-50879G>T		intron_variant			XP_016876324.1
LOC102723406	XR_001749811.2	n.250+4408C>A		intron_variant
LOC102723406	XR_007063750.1	n.353+4408C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000454681.2	n.92-50879G>T		intron_variant		5
ENSG00000230490	ENST00000686875.1	n.144-50879G>T		intron_variant

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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.252

Alfa AF: 0.184 Hom.: 1327

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928393; hg19: chr13-34149388;