13-33115601-G-A

Variant names:

• chr13-33115601-G-A
• rs538874
• NM_178006.4:c.2281+2464C>T

Variant summary

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

The NM_178006.4(STARD13):​c.2281+2464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,048 control chromosomes in the GnomAD database, including 4,209 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 0.23 (4209 hom., cov: 32)
• Consequence: STARD13 NM_178006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 2 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178006.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD13	NM_178006.4	MANE Select	c.2281+2464C>T		intron	N/A	NP_821074.1
	STARD13	NM_178007.3		c.2257+2464C>T		intron	N/A	NP_821075.1
	STARD13	NM_001411014.1		c.2236+2464C>T		intron	N/A	NP_001397943.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD13	ENST00000336934.10	TSL:1 MANE Select	c.2281+2464C>T		intron	N/A	ENSP00000338785.4
	STARD13	ENST00000255486.8	TSL:1	c.2257+2464C>T		intron	N/A	ENSP00000255486.4
	STARD13	ENST00000567873.2	TSL:1	c.2236+2464C>T		intron	N/A	ENSP00000456233.2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34543 AN: 151930 Hom.: 4198 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.227 AC: 34587 AN: 152048 Hom.: 4209 Cov.: 32 AF XY: 0.223 AC XY: 16568 AN XY: 74340

African (AFR) AF: 0.298 AC: 12368 AN: 41454

American (AMR) AF: 0.185 AC: 2830 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1628 AN: 5162

South Asian (SAS) AF: 0.185 AC: 890 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10586

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14019 AN: 67968

Other (OTH) AF: 0.228 AC: 480 AN: 2108

Alfa AF: 0.205 Hom.: 1961

Bravo AF: 0.232

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.16
DANN	Benign	0.57
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs538874; hg19: chr13-33689738;