13-33106808-C-T

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_178006.4(STARD13):c.3174G>A(p.Pro1058=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00432 in 1,614,036 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0035 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0044 (21 hom.)
• Consequence: STARD13 NM_178006.4 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -5.43

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 -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 13-33106808-C-T is Benign according to our data. Variant chr13-33106808-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 791588.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-5.43 with no splicing effect.
• BS2: High Homozygotes in GnomAd at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STARD13	NM_178006.4	c.3174G>A	p.Pro1058=	synonymous_variant	13/14	ENST00000336934.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STARD13	ENST00000336934.10	c.3174G>A	p.Pro1058=	synonymous_variant	13/14	1	NM_178006.4	P4
STARD13	ENST00000255486.8	c.3150G>A	p.Pro1050=	synonymous_variant	13/14	1		A2
STARD13	ENST00000567873.2	c.3129G>A	p.Pro1043=	synonymous_variant	13/14	1		A2
STARD13	ENST00000399365.7	c.2820G>A	p.Pro940=	synonymous_variant	13/14	1

Frequencies

GnomAD3 genomes AF: 0.00346 AC: 527 AN: 152210 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.000700

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00144

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00810

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00513

Gnomad OTH AF: 0.00383

GnomAD3 exomes AF: 0.00437 AC: 1097 AN: 250878 Hom.: 8 AF XY: 0.00409 AC XY: 555 AN XY: 135532

Gnomad AFR exome AF: 0.000984

Gnomad AMR exome AF: 0.00214

Gnomad ASJ exome AF: 0.00735

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000393

Gnomad FIN exome AF: 0.00809

Gnomad NFE exome AF: 0.00625

Gnomad OTH exome AF: 0.00620

GnomAD4 exome AF: 0.00441 AC: 6449 AN: 1461708 Hom.: 21 Cov.: 31 AF XY: 0.00428 AC XY: 3114 AN XY: 727144

Gnomad4 AFR exome AF: 0.000657

Gnomad4 AMR exome AF: 0.00204

Gnomad4 ASJ exome AF: 0.00754

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000568

Gnomad4 FIN exome AF: 0.00754

Gnomad4 NFE exome AF: 0.00482

Gnomad4 OTH exome AF: 0.00474

GnomAD4 genome AF: 0.00346 AC: 527 AN: 152328 Hom.: 3 Cov.: 33 AF XY: 0.00381 AC XY: 284 AN XY: 74482

Gnomad4 AFR AF: 0.000698

Gnomad4 AMR AF: 0.00144

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00810

Gnomad4 NFE AF: 0.00513

Gnomad4 OTH AF: 0.00379

Alfa AF: 0.00440 Hom.: 2

Bravo AF: 0.00302

Asia WGS AF: 0.000289 AC: 1 AN: 3476

EpiCase AF: 0.00469

EpiControl AF: 0.00564

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2022	STARD13: BP4, BP7 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Apr 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	0.48
Dann	Benign	0.43

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: rs117237914; hg19: chr13-33680945; COSMIC: COSV55229933; COSMIC: COSV55229933;