chr13-33560672-C-A

Variant names:

• chr13-33560672-C-A
• rs7998352
• NM_001243476.3:c.-105-36300G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001243476.3(STARD13):​c.-105-36300G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,060 control chromosomes in the GnomAD database, including 5,393 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 (5393 hom., cov: 32)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.-105-36300G>T		intron_variant	Intron 3 of 17		NP_001230405.1
STARD13	XM_017020835.3	c.-105-36300G>T		intron_variant	Intron 1 of 15		XP_016876324.1
LOC102723406	XR_001749811.2	n.68+5855C>A		intron_variant	Intron 1 of 4
LOC102723406	XR_007063750.1	n.85+5855C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000454681.2	n.92-36300G>T		intron_variant	Intron 1 of 5	5
ENSG00000230490	ENST00000686875.1	n.144-36300G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35801 AN: 150942 Hom.: 5355 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.238 AC: 35893 AN: 151060 Hom.: 5393 Cov.: 32 AF XY: 0.236 AC XY: 17463 AN XY: 73868

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.245

Alfa AF: 0.185 Hom.: 2678

Bravo AF: 0.253

Asia WGS AF: 0.293 AC: 1017 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.62
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7998352; hg19: chr13-34134809;