rs2555603

chr13-33224125-A-Cchr13-33224125-A-T

Variant summary

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

The NM_178006.4(STARD13):c.170-56503T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,132 control chromosomes in the GnomAD database, including 3,719 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 0.21 (3719 hom., cov: 32)
• Consequence: STARD13 NM_178006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

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-AS (HGNC:40873): (STARD13 antisense RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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/exons	MANE	UniProt
STARD13	NM_178006.4	c.170-56503T>G		intron_variant		ENST00000336934.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STARD13	ENST00000336934.10	c.170-56503T>G		intron_variant		1	NM_178006.4	P4
STARD13-AS	ENST00000628131.2	n.226+35868A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32077 AN: 152014 Hom.: 3714 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.211 AC: 32085 AN: 152132 Hom.: 3719 Cov.: 32 AF XY: 0.213 AC XY: 15843 AN XY: 74362

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.221

Alfa AF: 0.244 Hom.: 9842

Bravo AF: 0.197

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.76

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: rs2555603; hg19: chr13-33798262;