rs534668

Variant names:

• chr11-72772835-G-A
• rs534668
• NM_006645.3:c.207+8140C>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.207+8140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,892 control chromosomes in the GnomAD database, including 8,563 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 0.32 (8563 hom., cov: 32)
• Consequence: STARD10 NM_006645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.883
• Publications: 10 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD10	NM_006645.3	c.207+8140C>T		intron_variant	Intron 2 of 6	ENST00000334805.11	NP_006636.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD10	ENST00000334805.11	c.207+8140C>T		intron_variant	Intron 2 of 6	1	NM_006645.3	ENSP00000335247.6

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48970 AN: 151774 Hom.: 8557 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.323 AC: 49009 AN: 151892 Hom.: 8563 Cov.: 32 AF XY: 0.331 AC XY: 24605 AN XY: 74232

African (AFR) AF: 0.425 AC: 17588 AN: 41404

American (AMR) AF: 0.209 AC: 3190 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3468

East Asian (EAS) AF: 0.155 AC: 798 AN: 5162

South Asian (SAS) AF: 0.428 AC: 2049 AN: 4792

European-Finnish (FIN) AF: 0.496 AC: 5231 AN: 10542

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18735 AN: 67932

Other (OTH) AF: 0.252 AC: 531 AN: 2108

Alfa AF: 0.269 Hom.: 10583

Bravo AF: 0.300

Asia WGS AF: 0.279 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		0.88
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs534668; hg19: chr11-72483880;