rs519790

Variant names:

• chr11-72793096-C-G
• rs519790
• NM_006645.3:c.-335G>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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]

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006645.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD10	NM_006645.3	MANE Select	c.-335G>C		5_prime_UTR	Exon 1 of 7	NP_006636.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD10	ENST00000334805.11	TSL:1 MANE Select	c.-335G>C		5_prime_UTR	Exon 1 of 7	ENSP00000335247.6
	STARD10	ENST00000538536.5	TSL:1	c.-335G>C		5_prime_UTR	Exon 1 of 7	ENSP00000440016.1
	STARD10	ENST00000543304.5	TSL:1	c.-221-114G>C		intron	N/A	ENSP00000438792.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 17 AN: 34

Other (OTH) AF: 0.125 AC: 1 AN: 8

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

African (AFR) AF: 0.378 AC: 15653 AN: 41452

American (AMR) AF: 0.315 AC: 4812 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1592 AN: 5174

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4820

European-Finnish (FIN) AF: 0.248 AC: 2620 AN: 10578

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22815 AN: 67980

Other (OTH) AF: 0.339 AC: 716 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		-0.30
PromoterAI		0.039	Neutral
Mutation Taster		=298/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs519790; hg19: chr11-72504141;