Variant chr17-39657827-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006804.4(STARD3):c.350G>A(p.Arg117Gln) variant causes a missense change. The variant allele was found at a frequency of 0.64 in 1,613,930 control chromosomes in the GnomAD database, including 340,167 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.52 ( 23729 hom., cov: 32)

Exomes 𝑓: 0.65 ( 316438 hom. )

Consequence

STARD3
NM_006804.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.80

Variant links:

Genes affected

STARD3 (HGNC:17579): (StAR related lipid transfer domain containing 3) This gene encodes a member of a subfamily of lipid trafficking proteins that are characterized by a C-terminal steroidogenic acute regulatory domain and an N-terminal metastatic lymph node 64 domain. The encoded protein localizes to the membranes of late endosomes and may be involved in exporting cholesterol. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

STARD3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.5651027E-6).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD3	NM_006804.4 linkuse as main transcript	c.350G>A	p.Arg117Gln	missense_variant	4/15	ENST00000336308.10	NP_006795.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD3	ENST00000336308.10 linkuse as main transcript	c.350G>A	p.Arg117Gln	missense_variant	4/15	1	NM_006804.4	ENSP00000337446	P1	Q14849-1

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79448

AN:

151986

Hom.:

23724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.738

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.683

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.692

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.553

GnomAD3 exomes

AF:

0.617

AC:

155180

AN:

251318

Hom.:

50338

AF XY:

0.636

AC XY:

86378

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.220

Gnomad AMR exome

AF:

0.584

Gnomad ASJ exome

AF:

0.691

Gnomad EAS exome

AF:

0.388

Gnomad SAS exome

AF:

0.735

Gnomad FIN exome

AF:

0.694

Gnomad NFE exome

AF:

0.668

Gnomad OTH exome

AF:

0.641

GnomAD4 exome

AF:

0.652

AC:

953637

AN:

1461826

Hom.:

316438

Cov.:

AF XY:

0.657

AC XY:

477481

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.219

Gnomad4 AMR exome

AF:

0.579

Gnomad4 ASJ exome

AF:

0.686

Gnomad4 EAS exome

AF:

0.461

Gnomad4 SAS exome

AF:

0.740

Gnomad4 FIN exome

AF:

0.686

Gnomad4 NFE exome

AF:

0.667

Gnomad4 OTH exome

AF:

0.634

GnomAD4 genome

AF:

0.522

AC:

79466

AN:

152104

Hom.:

23729

Cov.:

AF XY:

0.524

AC XY:

38951

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.225

Gnomad4 AMR

AF:

0.537

Gnomad4 ASJ

AF:

0.683

Gnomad4 EAS

AF:

0.417

Gnomad4 SAS

AF:

0.706

Gnomad4 FIN

AF:

0.692

Gnomad4 NFE

AF:

0.657

Gnomad4 OTH

AF:

0.553

Alfa

AF:

0.640

Hom.:

77185

Bravo

AF:

0.496

TwinsUK

AF:

0.662

AC:

2453

ALSPAC

AF:

0.654

AC:

2520

ESP6500AA

AF:

0.237

AC:

1043

ESP6500EA

AF:

0.653

AC:

5613

ExAC

AF:

0.614

AC:

74570

Asia WGS

AF:

0.588

AC:

2042

AN:

3476

EpiCase

AF:

0.675

EpiControl

AF:

0.668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.36

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.14

T;.;.;.;.;T;.;T;.

Eigen

Benign

0.035

Eigen_PC

Benign

0.12

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.83

T;D;T;T;T;T;T;T;T

MetaRNN

Benign

0.0000046

T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

2.0

M;M;.;M;.;.;.;.;.

MutationTaster

Benign

8.7e-7

P;P;P;P

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-1.5

N;N;.;N;.;.;.;.;N

REVEL

Benign

0.16

Sift

Benign

0.24

T;T;.;T;.;.;.;.;T

Sift4G

Benign

0.065

T;T;T;T;T;T;T;T;T

Polyphen

0.13

B;.;.;.;.;.;.;.;.

Vest4

0.40

MPC

0.55

ClinPred

0.029

GERP RS

4.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.18

gMVP

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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