Variant rs3817160 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.-52+331C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,956 control chromosomes in the GnomAD database, including 31,598 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 0.61 ( 31582 hom., cov: 30)

Exomes 𝑓: 0.84 ( 16 hom. )

Consequence

STARD3
NM_006804.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.457

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:

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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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STARD3	NM_006804.4 linkuse as main transcript	c.-52+331C>G		intron_variant		ENST00000336308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STARD3	ENST00000336308.10 linkuse as main transcript	c.-52+331C>G		intron_variant		1	NM_006804.4	P1	Q14849-1

Frequencies

GnomAD3 genomes

AF:

0.609

AC:

92387

AN:

151794

Hom.:

31575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.748

Gnomad AMR

AF:

0.614

Gnomad ASJ

AF:

0.739

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.779

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.768

Gnomad OTH

AF:

0.640

GnomAD4 exome

AF:

0.841

AC:

AN:

Hom.:

Cov.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.929

Gnomad4 NFE exome

AF:

0.875

Gnomad4 OTH exome

AF:

0.900

GnomAD4 genome

AF:

0.608

AC:

92417

AN:

151912

Hom.:

31582

Cov.:

AF XY:

0.608

AC XY:

45128

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.291

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.739

Gnomad4 EAS

AF:

0.440

Gnomad4 SAS

AF:

0.722

Gnomad4 FIN

AF:

0.779

Gnomad4 NFE

AF:

0.768

Gnomad4 OTH

AF:

0.640

Alfa

AF:

0.564

Hom.:

1909

Bravo

AF:

0.581

Asia WGS

AF:

0.606

AC:

2108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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