Variant 8-38146269-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000349.3(STAR):c.465+20A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.985 in 1,614,026 control chromosomes in the GnomAD database, including 783,079 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.98 ( 72617 hom., cov: 31)

Exomes 𝑓: 0.99 ( 710462 hom. )

Consequence

STAR
NM_000349.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.0580

Variant links:

Genes affected

STAR (HGNC:11359): (steroidogenic acute regulatory protein) The protein encoded by this gene plays a key role in the acute regulation of steroid hormone synthesis by enhancing the conversion of cholesterol into pregnenolone. This protein permits the cleavage of cholesterol into pregnenolone by mediating the transport of cholesterol from the outer mitochondrial membrane to the inner mitochondrial membrane. Mutations in this gene are a cause of congenital lipoid adrenal hyperplasia (CLAH), also called lipoid CAH. A pseudogene of this gene is located on chromosome 13. [provided by RefSeq, Jul 2008]

STAR links:

STAR (HGNC:):

STAR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 8-38146269-T-C is Benign according to our data. Variant chr8-38146269-T-C is described in ClinVar as [Benign]. Clinvar id is 448532.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-38146269-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAR	NM_000349.3 linkuse as main transcript	c.465+20A>G		intron_variant		ENST00000276449.9	NP_000340.2	P49675Q6IBK0

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
STAR	ENST00000276449.9 linkuse as main transcript	c.465+20A>G	intron_variant	1	NM_000349.3	ENSP00000276449.3	P49675
STAR	ENST00000522050.1 linkuse as main transcript	c.399+20A>G	intron_variant	5		ENSP00000429009.1	H0YB94
STAR	ENST00000520114.1 linkuse as main transcript	n.952+20A>G	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.976

AC:

148547

AN:

152158

Hom.:

72569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.946

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.987

Gnomad ASJ

AF:

0.976

Gnomad EAS

AF:

0.995

Gnomad SAS

AF:

0.935

Gnomad FIN

AF:

0.994

Gnomad MID

AF:

0.991

Gnomad NFE

AF:

0.990

Gnomad OTH

AF:

0.981

GnomAD3 exomes

AF:

0.981

AC:

246568

AN:

251294

Hom.:

121023

AF XY:

0.980

AC XY:

133121

AN XY:

135830

show subpopulations

Gnomad AFR exome

AF:

0.946

Gnomad AMR exome

AF:

0.993

Gnomad ASJ exome

AF:

0.977

Gnomad EAS exome

AF:

0.997

Gnomad SAS exome

AF:

0.935

Gnomad FIN exome

AF:

0.994

Gnomad NFE exome

AF:

0.990

Gnomad OTH exome

AF:

0.981

GnomAD4 exome

AF:

0.986

AC:

1440978

AN:

1461750

Hom.:

710462

Cov.:

AF XY:

0.985

AC XY:

716129

AN XY:

727178

show subpopulations

Gnomad4 AFR exome

AF:

0.944

Gnomad4 AMR exome

AF:

0.991

Gnomad4 ASJ exome

AF:

0.979

Gnomad4 EAS exome

AF:

0.989

Gnomad4 SAS exome

AF:

0.938

Gnomad4 FIN exome

AF:

0.994

Gnomad4 NFE exome

AF:

0.990

Gnomad4 OTH exome

AF:

0.982

GnomAD4 genome

AF:

0.976

AC:

148652

AN:

152276

Hom.:

72617

Cov.:

AF XY:

0.976

AC XY:

72697

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.946

Gnomad4 AMR

AF:

0.987

Gnomad4 ASJ

AF:

0.976

Gnomad4 EAS

AF:

0.995

Gnomad4 SAS

AF:

0.934

Gnomad4 FIN

AF:

0.994

Gnomad4 NFE

AF:

0.990

Gnomad4 OTH

AF:

0.980

Alfa

AF:

0.982

Hom.:

13629

Bravo

AF:

0.976

Asia WGS

AF:

0.934

AC:

3251

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 08, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 27, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 10, 2021	- -

Congenital lipoid adrenal hyperplasia due to STAR deficency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

8.0

DANN

Benign

0.34

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over