13-33648124-C-A

Position:

• chr13-33648124-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001243476.3(STARD13):​c.-106+13153G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,156 control chromosomes in the GnomAD database, including 77 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 0.031 (77 hom., cov: 32)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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=-0.9).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0307 (4665/152156) while in subpopulation AFR AF= 0.0513 (2129/41486). AF 95% confidence interval is 0.0495. There are 77 homozygotes in gnomad4. There are 2271 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 77 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.-106+13153G>T		intron_variant			NP_001230405.1
STARD13	XM_017020835.3	c.-106+28554G>T		intron_variant			XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000454681.2	n.91+28554G>T		intron_variant		5
ENSG00000230490	ENST00000653421.1	n.94-13125G>T		intron_variant
ENSG00000230490	ENST00000654283.1	n.569+8688G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4664 AN: 152038 Hom.: 77 Cov.: 32

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00560

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0229

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0307 AC: 4665 AN: 152156 Hom.: 77 Cov.: 32 AF XY: 0.0305 AC XY: 2271 AN XY: 74402

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.0228

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00560

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.0229

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0260 Hom.: 16

Bravo AF: 0.0305

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8001893; hg19: chr13-34222261;