rs4943110

Variant names:

• chr13-33461723-T-A
• rs4943110
• NM_001243476.3:c.31-21999A>T

Variant summary

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

The NM_001243476.3(STARD13):​c.31-21999A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,030 control chromosomes in the GnomAD database, including 7,632 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 (7632 hom., cov: 32)
• Consequence: STARD13 NM_001243476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 1 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=-0.96).
• 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.31-21999A>T		intron_variant	Intron 4 of 17		NP_001230405.1
STARD13	XM_047430759.1	c.166-21999A>T		intron_variant	Intron 2 of 15		XP_047286715.1
STARD13	XM_017020835.3	c.31-21999A>T		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.227-21999A>T		intron_variant	Intron 2 of 5	5
ENSG00000230490	ENST00000686875.1	n.279-21999A>T		intron_variant	Intron 2 of 3
ENSG00000230490	ENST00000730869.1	n.630-21999A>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45755 AN: 151912 Hom.: 7634 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.301 AC: 45767 AN: 152030 Hom.: 7632 Cov.: 32 AF XY: 0.296 AC XY: 21967 AN XY: 74304

African (AFR) AF: 0.153 AC: 6333 AN: 41474

American (AMR) AF: 0.326 AC: 4967 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5172

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4822

European-Finnish (FIN) AF: 0.310 AC: 3277 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26409 AN: 67960

Other (OTH) AF: 0.316 AC: 666 AN: 2110

Alfa AF: 0.336 Hom.: 1148

Bravo AF: 0.297

Asia WGS AF: 0.234 AC: 815 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.2
DANN	Benign	0.68
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs4943110; hg19: chr13-34035860;