13-33138648-G-A

Variant names:

• chr13-33138648-G-A
• rs7322586
• ENST00000487412.5:n.720C>T

Variant summary

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

The ENST00000487412.5(STARD13):​n.720C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 271,552 control chromosomes in the GnomAD database, including 1,298 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 0.095 (830 hom., cov: 32)
  • Exomes 𝑓: 0.078 (468 hom.)
• Consequence: STARD13 ENST00000487412.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487412.5. 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.387+3662C>T		intron	N/A	NP_821074.1
	STARD13	NM_178007.3		c.363+3662C>T		intron	N/A	NP_821075.1
	STARD13	NM_001411014.1		c.342+3662C>T		intron	N/A	NP_001397943.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD13	ENST00000487412.5	TSL:1	n.720C>T		non_coding_transcript_exon	Exon 5 of 5
	STARD13	ENST00000336934.10	TSL:1 MANE Select	c.387+3662C>T		intron	N/A	ENSP00000338785.4
	STARD13	ENST00000255486.8	TSL:1	c.363+3662C>T		intron	N/A	ENSP00000255486.4

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14392 AN: 152076 Hom.: 829 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.0783 AC: 9344 AN: 119358 Hom.: 468 Cov.: 0 AF XY: 0.0808 AC XY: 5246 AN XY: 64956

African (AFR) AF: 0.102 AC: 234 AN: 2288

American (AMR) AF: 0.125 AC: 504 AN: 4030

Ashkenazi Jewish (ASJ) AF: 0.0699 AC: 195 AN: 2788

East Asian (EAS) AF: 0.226 AC: 721 AN: 3188

South Asian (SAS) AF: 0.0954 AC: 2314 AN: 24250

European-Finnish (FIN) AF: 0.0938 AC: 720 AN: 7676

Middle Eastern (MID) AF: 0.0648 AC: 28 AN: 432

European-Non Finnish (NFE) AF: 0.0608 AC: 4171 AN: 68596

Other (OTH) AF: 0.0748 AC: 457 AN: 6110

GnomAD4 genome AF: 0.0947 AC: 14414 AN: 152194 Hom.: 830 Cov.: 32 AF XY: 0.0963 AC XY: 7168 AN XY: 74410

African (AFR) AF: 0.115 AC: 4781 AN: 41532

American (AMR) AF: 0.126 AC: 1922 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1267 AN: 5156

South Asian (SAS) AF: 0.0956 AC: 461 AN: 4822

European-Finnish (FIN) AF: 0.0943 AC: 1000 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0650 AC: 4423 AN: 68008

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.0788 Hom.: 1457

Bravo AF: 0.102

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.86
PhyloP100		0.38
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: rs7322586; hg19: chr13-33712785;