13-33126237-T-G

Variant names:

• chr13-33126237-T-G
• rs1980781
• NM_178006.4:c.1926A>C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_178006.4(STARD13):​c.1926A>C​(p.Ser642Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,613,250 control chromosomes in the GnomAD database, including 45,492 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 (4359 hom., cov: 32)
  • Exomes 𝑓: 0.23 (41133 hom.)
• Consequence: STARD13 NM_178006.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

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]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BP7: Synonymous conserved (PhyloP=0.338 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_178006.4	c.1926A>C	p.Ser642Ser	synonymous_variant	Exon 7 of 14	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.1926A>C	p.Ser642Ser	synonymous_variant	Exon 7 of 14	1	NM_178006.4	ENSP00000338785.4
STARD13	ENST00000255486.8	c.1902A>C	p.Ser634Ser	synonymous_variant	Exon 7 of 14	1		ENSP00000255486.4
STARD13	ENST00000567873.2	c.1881A>C	p.Ser627Ser	synonymous_variant	Exon 7 of 14	1		ENSP00000456233.2
STARD13	ENST00000399365.7	c.1572A>C	p.Ser524Ser	synonymous_variant	Exon 7 of 14	1		ENSP00000382300.3

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35477 AN: 152012 Hom.: 4349 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.214

GnomAD3 exomes AF: 0.252 AC: 63374 AN: 251314 Hom.: 8344 AF XY: 0.251 AC XY: 34153 AN XY: 135838

Gnomad AFR exome AF: 0.216

Gnomad AMR exome AF: 0.327

Gnomad ASJ exome AF: 0.203

Gnomad EAS exome AF: 0.223

Gnomad SAS exome AF: 0.291

Gnomad FIN exome AF: 0.332

Gnomad NFE exome AF: 0.219

Gnomad OTH exome AF: 0.232

GnomAD4 exome AF: 0.234 AC: 342596 AN: 1461120 Hom.: 41133 Cov.: 34 AF XY: 0.235 AC XY: 171001 AN XY: 726802

Gnomad4 AFR exome AF: 0.219

Gnomad4 AMR exome AF: 0.322

Gnomad4 ASJ exome AF: 0.203

Gnomad4 EAS exome AF: 0.234

Gnomad4 SAS exome AF: 0.284

Gnomad4 FIN exome AF: 0.329

Gnomad4 NFE exome AF: 0.224

Gnomad4 OTH exome AF: 0.229

GnomAD4 genome AF: 0.233 AC: 35507 AN: 152130 Hom.: 4359 Cov.: 32 AF XY: 0.241 AC XY: 17905 AN XY: 74368

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.211

Alfa AF: 0.217 Hom.: 8540

Bravo AF: 0.228

Asia WGS AF: 0.249 AC: 867 AN: 3478

EpiCase AF: 0.219

EpiControl AF: 0.221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	5.4
DANN	Benign	0.72

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: rs1980781; hg19: chr13-33700374; COSMIC: COSV55231352; COSMIC: COSV55231352;