13-33106717-T-G

Variant names:

• chr13-33106717-T-G
• rs642899
• NM_178006.4:c.3224+41A>C

Variant summary

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

The NM_178006.4(STARD13):​c.3224+41A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,540,296 control chromosomes in the GnomAD database, including 44,564 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 (4107 hom., cov: 32)
  • Exomes 𝑓: 0.24 (40457 hom.)
• Consequence: STARD13 NM_178006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 12 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_178006.4	c.3224+41A>C		intron_variant	Intron 13 of 13	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.3224+41A>C		intron_variant	Intron 13 of 13	1	NM_178006.4	ENSP00000338785.4
STARD13	ENST00000255486.8	c.3200+41A>C		intron_variant	Intron 13 of 13	1		ENSP00000255486.4
STARD13	ENST00000567873.2	c.3179+41A>C		intron_variant	Intron 13 of 13	1		ENSP00000456233.2
STARD13	ENST00000399365.7	c.2870+41A>C		intron_variant	Intron 13 of 13	1		ENSP00000382300.3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34392 AN: 151820 Hom.: 4101 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.209

GnomAD2 exomes AF: 0.247 AC: 52674 AN: 212948 AF XY: 0.250

Gnomad AFR exome AF: 0.185

Gnomad AMR exome AF: 0.283

Gnomad ASJ exome AF: 0.195

Gnomad EAS exome AF: 0.195

Gnomad FIN exome AF: 0.351

Gnomad NFE exome AF: 0.229

Gnomad OTH exome AF: 0.233

GnomAD4 exome AF: 0.238 AC: 330354 AN: 1388358 Hom.: 40457 Cov.: 27 AF XY: 0.239 AC XY: 163695 AN XY: 683634

African (AFR) AF: 0.190 AC: 6024 AN: 31776

American (AMR) AF: 0.276 AC: 10687 AN: 38738

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 4453 AN: 22824

East Asian (EAS) AF: 0.202 AC: 7700 AN: 38046

South Asian (SAS) AF: 0.296 AC: 22037 AN: 74494

European-Finnish (FIN) AF: 0.347 AC: 17793 AN: 51300

Middle Eastern (MID) AF: 0.173 AC: 939 AN: 5440

European-Non Finnish (NFE) AF: 0.232 AC: 247598 AN: 1068632

Other (OTH) AF: 0.230 AC: 13123 AN: 57108

GnomAD4 genome AF: 0.226 AC: 34412 AN: 151938 Hom.: 4107 Cov.: 32 AF XY: 0.234 AC XY: 17339 AN XY: 74244

African (AFR) AF: 0.185 AC: 7654 AN: 41418

American (AMR) AF: 0.239 AC: 3652 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1014 AN: 5160

South Asian (SAS) AF: 0.310 AC: 1491 AN: 4808

European-Finnish (FIN) AF: 0.365 AC: 3847 AN: 10536

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15561 AN: 67960

Other (OTH) AF: 0.207 AC: 437 AN: 2110

Alfa AF: 0.226 Hom.: 2954

Bravo AF: 0.215

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.16
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs642899; hg19: chr13-33680854; COSMIC: COSV55227569;