chr13-33523513-C-T

Position:

• chr13-33523513-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.30+725G>A		intron_variant			NP_001230405.1
STARD13	XM_047430759.1	c.165+725G>A		intron_variant			XP_047286715.1
STARD13	XM_017020835.3	c.30+725G>A		intron_variant			XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000437698.1	n.85+725G>A		intron_variant		3
ENSG00000230490	ENST00000454681.2	n.226+725G>A		intron_variant		5
ENSG00000230490	ENST00000686875.1	n.278+725G>A		intron_variant

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

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.448

Alfa AF: 0.472 Hom.: 21657

Bravo AF: 0.421

Asia WGS AF: 0.458 AC: 1589 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943116; hg19: chr13-34097650;