chr13-33488440-A-G

Position:

• chr13-33488440-A-G

Variant summary

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

The NM_001243476.3(STARD13):​c.30+35798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 152,288 control chromosomes in the GnomAD database, including 1,102 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 0.075 (1102 hom., cov: 32)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.30+35798T>C		intron_variant			NP_001230405.1
STARD13	XM_047430759.1	c.165+35798T>C		intron_variant			XP_047286715.1
STARD13	XM_017020835.3	c.30+35798T>C		intron_variant			XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000454681.2	n.226+35798T>C		intron_variant		5
ENSG00000230490	ENST00000686875.1	n.278+35798T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11348 AN: 152170 Hom.: 1088 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.0809

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00613

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0748 AC: 11392 AN: 152288 Hom.: 1102 Cov.: 32 AF XY: 0.0744 AC XY: 5540 AN XY: 74470

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0303

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.0805

Gnomad4 SAS AF: 0.0563

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.00612

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0443 Hom.: 80

Bravo AF: 0.0804

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315218; hg19: chr13-34062577;