rs519790

Positions:

• chr11-72793096-C-G
• chr11-72793096-C-T

Variant summary

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

The NM_006645.3(STARD10):​c.-335G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,110 control chromosomes in the GnomAD database, including 8,720 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 0.34 (8717 hom., cov: 33)
  • Exomes 𝑓: 0.38 (3 hom.)
• Consequence: STARD10 NM_006645.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

Genes affected

STARD10 (HGNC:10666): (StAR related lipid transfer domain containing 10) Predicted to enable lipid binding activity. Predicted to be involved in lipid transport. Predicted to act upstream of or within bile acid secretion and positive regulation of peroxisome proliferator activated receptor signaling pathway. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

STARD10 (HGNC:):

ARAP1 (HGNC:16925): (ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1) The protein encoded by this gene contains SAM, ARF-GAP, RHO-GAP, ankyrin repeat, RAS-associating, and pleckstrin homology (PH) domains. In vitro, this protein displays RHO-GAP and phosphatidylinositol (3,4,5) trisphosphate (PIP3)-dependent ARF-GAP activity. The encoded protein associates with the Golgi, and the ARF-GAP activity mediates changes in the Golgi and the formation of filopodia. It is thought to regulate the cell-specific trafficking of a receptor protein involved in apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD10	NM_006645.3	c.-335G>C		5_prime_UTR_variant	1/7	ENST00000334805.11	NP_006636.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD10	ENST00000334805.11	c.-335G>C		5_prime_UTR_variant	1/7	1	NM_006645.3	ENSP00000335247.6

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50934 AN: 151938 Hom.: 8702 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.340

GnomAD4 exome AF: 0.385 AC: 20 AN: 52 Hom.: 3 Cov.: 0 AF XY: 0.395 AC XY: 15 AN XY: 38

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.335 AC: 50985 AN: 152058 Hom.: 8717 Cov.: 33 AF XY: 0.329 AC XY: 24425 AN XY: 74338

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.339

Alfa AF: 0.324 Hom.: 1059

Bravo AF: 0.346

Asia WGS AF: 0.295 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.72

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

Other links and lift over

dbSNP: rs519790; hg19: chr11-72504141;