rs9892427

chr17-39648605-T-C

Variant summary

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

The NM_006804.4(STARD3):c.-51-4876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,148 control chromosomes in the GnomAD database, including 2,069 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 0.13 (2069 hom., cov: 31)
• Consequence: STARD3 NM_006804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STARD3	NM_006804.4	c.-51-4876T>C		intron_variant		ENST00000336308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STARD3	ENST00000336308.10	c.-51-4876T>C		intron_variant		1	NM_006804.4	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19813 AN: 152030 Hom.: 2059 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0434

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.131 AC: 19873 AN: 152148 Hom.: 2069 Cov.: 31 AF XY: 0.127 AC XY: 9449 AN XY: 74396

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.0712

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0428

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0830 Hom.: 949

Bravo AF: 0.138

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.15
Dann	Benign	0.75

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: rs9892427; hg19: chr17-37804858;