Variant 13-33106717-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178006.4(STARD13):c.3224+41A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,540,296 control chromosomes in the GnomAD database, including 44,564 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 ( 4107 hom., cov: 32)

Exomes 𝑓: 0.24 ( 40457 hom. )

Consequence

STARD13
NM_178006.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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	Protein	UniProt
STARD13	NM_178006.4 linkuse as main transcript	c.3224+41A>C		intron_variant		ENST00000336934.10	NP_821074.1	Q9Y3M8-1A0A024RDV4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
STARD13	ENST00000336934.10 linkuse as main transcript	c.3224+41A>C	intron_variant	1	NM_178006.4	ENSP00000338785.4	Q9Y3M8-1
STARD13	ENST00000255486.8 linkuse as main transcript	c.3200+41A>C	intron_variant	1		ENSP00000255486.4	Q9Y3M8-2
STARD13	ENST00000567873.2 linkuse as main transcript	c.3179+41A>C	intron_variant	1		ENSP00000456233.2	H3BRG5
STARD13	ENST00000399365.7 linkuse as main transcript	c.2870+41A>C	intron_variant	1		ENSP00000382300.3	Q9Y3M8-3

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34392

AN:

151820

Hom.:

4101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.196

Gnomad SAS

AF:

0.312

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.209

GnomAD3 exomes

AF:

0.247

AC:

52674

AN:

212948

Hom.:

6861

AF XY:

0.250

AC XY:

28453

AN XY:

114000

show subpopulations

Gnomad AFR exome

AF:

0.185

Gnomad AMR exome

AF:

0.283

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.195

Gnomad SAS exome

AF:

0.298

Gnomad FIN exome

AF:

0.351

Gnomad NFE exome

AF:

0.229

Gnomad OTH exome

AF:

0.233

GnomAD4 exome

AF:

0.238

AC:

330354

AN:

1388358

Hom.:

40457

Cov.:

AF XY:

0.239

AC XY:

163695

AN XY:

683634

show subpopulations

Gnomad4 AFR exome

AF:

0.190

Gnomad4 AMR exome

AF:

0.276

Gnomad4 ASJ exome

AF:

0.195

Gnomad4 EAS exome

AF:

0.202

Gnomad4 SAS exome

AF:

0.296

Gnomad4 FIN exome

AF:

0.347

Gnomad4 NFE exome

AF:

0.232

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.226

AC:

34412

AN:

151938

Hom.:

4107

Cov.:

AF XY:

0.234

AC XY:

17339

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.310

Gnomad4 FIN

AF:

0.365

Gnomad4 NFE

AF:

0.229

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.227

Hom.:

2132

Bravo

AF:

0.215

Asia WGS

AF:

0.234

AC:

814

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over