rs16887217

Positions:

• chr8-38146907-T-C
• chr8-38146907-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000349.3(STAR):​c.307-460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 151,822 control chromosomes in the GnomAD database, including 124 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 0.011 (124 hom., cov: 30)
• Consequence: STAR NM_000349.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAR	NM_000349.3	c.307-460A>G		intron_variant		ENST00000276449.9	NP_000340.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAR	ENST00000276449.9	c.307-460A>G		intron_variant		1	NM_000349.3	ENSP00000276449.3
STAR	ENST00000522050.1	c.241-460A>G		intron_variant		5		ENSP00000429009.1
STAR	ENST00000521236.1	c.61-460A>G		intron_variant		3		ENSP00000430030.1
STAR	ENST00000520114.1	n.794-460A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0115 AC: 1743 AN: 151726 Hom.: 126 Cov.: 30

Gnomad AFR AF: 0.00116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00184

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.00730

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.00116

Gnomad OTH AF: 0.00909

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0114 AC: 1737 AN: 151822 Hom.: 124 Cov.: 30 AF XY: 0.0146 AC XY: 1084 AN XY: 74192

Gnomad4 AFR AF: 0.00116

Gnomad4 AMR AF: 0.00184

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.00730

Gnomad4 NFE AF: 0.00116

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.00276 Hom.: 16

Bravo AF: 0.00738

Asia WGS AF: 0.136 AC: 471 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.36

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

Other links and lift over

dbSNP: rs16887217; hg19: chr8-38004425;