13-33487438-A-C

Variant names:

• chr13-33487438-A-C
• rs7981602
• NM_001243476.3:c.30+36800T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001243476.3(STARD13):​c.30+36800T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,052 control chromosomes in the GnomAD database, including 7,644 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 0.30 (7644 hom., cov: 31)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 3 publications found

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]

STARD13 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000230490 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.30+36800T>G		intron_variant	Intron 4 of 17		NP_001230405.1
STARD13	XM_047430759.1	c.165+36800T>G		intron_variant	Intron 2 of 15		XP_047286715.1
STARD13	XM_017020835.3	c.30+36800T>G		intron_variant	Intron 2 of 15		XP_016876324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230490	ENST00000454681.2	n.226+36800T>G		intron_variant	Intron 2 of 5	5
ENSG00000230490	ENST00000686875.1	n.278+36800T>G		intron_variant	Intron 2 of 3
ENSG00000230490	ENST00000730869.1	n.629+36800T>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45396 AN: 151934 Hom.: 7645 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.299 AC: 45394 AN: 152052 Hom.: 7644 Cov.: 31 AF XY: 0.294 AC XY: 21856 AN XY: 74310

African (AFR) AF: 0.139 AC: 5765 AN: 41514

American (AMR) AF: 0.328 AC: 5008 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3468

East Asian (EAS) AF: 0.209 AC: 1082 AN: 5174

South Asian (SAS) AF: 0.326 AC: 1575 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3291 AN: 10554

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26450 AN: 67936

Other (OTH) AF: 0.320 AC: 675 AN: 2112

Alfa AF: 0.327 Hom.: 1157

Bravo AF: 0.293

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.71
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs7981602; hg19: chr13-34061575;