NM_001243476.3:c.31-23202C>G

Variant names:

• chr13-33462926-G-C
• rs1886870
• NM_001243476.3:c.31-23202C>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.31-23202C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,960 control chromosomes in the GnomAD database, including 18,136 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 0.49 (18136 hom., cov: 31)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 5 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_001243476.3	c.31-23202C>G		intron_variant	Intron 4 of 17		NP_001230405.1
STARD13	XM_047430759.1	c.166-23202C>G		intron_variant	Intron 2 of 15		XP_047286715.1
STARD13	XM_017020835.3	c.31-23202C>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.227-23202C>G		intron_variant	Intron 2 of 5	5
ENSG00000230490	ENST00000686875.1	n.279-23202C>G		intron_variant	Intron 2 of 3
ENSG00000230490	ENST00000730869.1	n.630-23202C>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73625 AN: 151842 Hom.: 18101 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.485 AC: 73720 AN: 151960 Hom.: 18136 Cov.: 31 AF XY: 0.478 AC XY: 35479 AN XY: 74258

African (AFR) AF: 0.563 AC: 23320 AN: 41450

American (AMR) AF: 0.465 AC: 7094 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2293 AN: 5172

South Asian (SAS) AF: 0.450 AC: 2166 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4041 AN: 10518

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31670 AN: 67956

Other (OTH) AF: 0.500 AC: 1054 AN: 2108

Alfa AF: 0.303 Hom.: 675

Bravo AF: 0.495

Asia WGS AF: 0.462 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.31
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1886870; hg19: chr13-34037063;