13-33134652-C-T

Variant names:

• chr13-33134652-C-T
• rs10492402
• NM_178006.4:c.388-4363G>A

Variant summary

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

The NM_178006.4(STARD13):​c.388-4363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,098 control chromosomes in the GnomAD database, including 626 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 0.081 (626 hom., cov: 33)
• Consequence: STARD13 NM_178006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_178006.4	c.388-4363G>A		intron_variant	Intron 4 of 13	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.388-4363G>A		intron_variant	Intron 4 of 13	1	NM_178006.4	ENSP00000338785.4
STARD13	ENST00000255486.8	c.364-4363G>A		intron_variant	Intron 4 of 13	1		ENSP00000255486.4
STARD13	ENST00000567873.2	c.343-4363G>A		intron_variant	Intron 4 of 13	1		ENSP00000456233.2
STARD13	ENST00000399365.7	c.34-4363G>A		intron_variant	Intron 4 of 13	1		ENSP00000382300.3

Frequencies

GnomAD3 genomes AF: 0.0811 AC: 12324 AN: 151980 Hom.: 626 Cov.: 33

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0811 AC: 12340 AN: 152098 Hom.: 626 Cov.: 33 AF XY: 0.0835 AC XY: 6210 AN XY: 74352

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.0951

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0727 Hom.: 235

Bravo AF: 0.0859

Asia WGS AF: 0.156 AC: 544 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	0.63
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492402; hg19: chr13-33708789;