rs7322586

Positions:

• chr13-33138648-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178006.4(STARD13):​c.387+3662C>T variant causes a intron 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 NM_178006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD13	NM_178006.4	c.387+3662C>T		intron_variant		ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.387+3662C>T		intron_variant		1	NM_178006.4	ENSP00000338785.4

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

Gnomad4 AFR exome AF: 0.102

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.0699

Gnomad4 EAS exome AF: 0.226

Gnomad4 SAS exome AF: 0.0954

Gnomad4 FIN exome AF: 0.0938

Gnomad4 NFE exome AF: 0.0608

Gnomad4 OTH exome AF: 0.0748

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

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0758

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.0956

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.0650

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0732 Hom.: 802

Bravo AF: 0.102

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs7322586; hg19: chr13-33712785;