Variant rs3742321 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.749A>G(p.Lys250Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,613,144 control chromosomes in the GnomAD database, including 43,207 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.21 ( 3600 hom., cov: 32)

Exomes 𝑓: 0.23 ( 39607 hom. )

Consequence

STARD13
NM_178006.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.27

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 (MetaRNN=0.0013130903).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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.749A>G	p.Lys250Arg	missense_variant	5/14	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10 linkuse as main transcript	c.749A>G	p.Lys250Arg	missense_variant	5/14	1	NM_178006.4	ENSP00000338785	P4	Q9Y3M8-1
STARD13	ENST00000255486.8 linkuse as main transcript	c.725A>G	p.Lys242Arg	missense_variant	5/14	1		ENSP00000255486	A2	Q9Y3M8-2
STARD13	ENST00000567873.2 linkuse as main transcript	c.704A>G	p.Lys235Arg	missense_variant	5/14	1		ENSP00000456233	A2
STARD13	ENST00000399365.7 linkuse as main transcript	c.395A>G	p.Lys132Arg	missense_variant	5/14	1		ENSP00000382300		Q9Y3M8-3

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31433

AN:

152014

Hom.:

3595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.205

GnomAD3 exomes

AF:

0.242

AC:

60504

AN:

250254

Hom.:

7789

AF XY:

0.242

AC XY:

32782

AN XY:

135338

show subpopulations

Gnomad AFR exome

AF:

0.123

Gnomad AMR exome

AF:

0.322

Gnomad ASJ exome

AF:

0.178

Gnomad EAS exome

AF:

0.223

Gnomad SAS exome

AF:

0.277

Gnomad FIN exome

AF:

0.330

Gnomad NFE exome

AF:

0.218

Gnomad OTH exome

AF:

0.224

GnomAD4 exome

AF:

0.229

AC:

335301

AN:

1461012

Hom.:

39607

Cov.:

AF XY:

0.230

AC XY:

167331

AN XY:

726808

show subpopulations

Gnomad4 AFR exome

AF:

0.125

Gnomad4 AMR exome

AF:

0.317

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.234

Gnomad4 SAS exome

AF:

0.271

Gnomad4 FIN exome

AF:

0.328

Gnomad4 NFE exome

AF:

0.223

Gnomad4 OTH exome

AF:

0.219

GnomAD4 genome

AF:

0.207

AC:

31444

AN:

152132

Hom.:

3600

Cov.:

AF XY:

0.215

AC XY:

15950

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.156

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.282

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.221

Gnomad4 OTH

AF:

0.202

Alfa

AF:

0.215

Hom.:

6845

Bravo

AF:

0.197

TwinsUK

AF:

0.217

AC:

804

ALSPAC

AF:

0.223

AC:

860

ESP6500AA

AF:

0.131

AC:

575

ESP6500EA

AF:

0.214

AC:

1839

ExAC

AF:

0.237

AC:

28816

Asia WGS

AF:

0.236

AC:

822

AN:

3478

EpiCase

AF:

0.217

EpiControl

AF:

0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.088

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.24

T;.;.;T

Eigen

Benign

0.0018

Eigen_PC

Benign

0.14

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.65

T;T;T;T

MetaRNN

Benign

0.0013

T;T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Uncertain

2.4

M;.;.;.

MutationTaster

Benign

0.000090

P;P;P

PrimateAI

Benign

0.43

PROVEAN

Benign

-2.0

N;N;N;N

REVEL

Benign

0.093

Sift

Benign

0.045

D;D;D;T

Sift4G

Benign

0.073

T;T;T;.

Polyphen

0.044

B;B;.;.

Vest4

0.046

MPC

0.12

ClinPred

0.021

GERP RS

4.4

Varity_R

0.091

gMVP

0.17

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