chr11-72757802-C-T

Variant names:

• chr11-72757802-C-T
• rs1858663557
• NM_006645.3:c.542G>A
• STARD10 p.Cys181Tyr

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+2 Uncertain · Warm

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 2 classification points (ACMG Germline Pathogenicity v2019). PM2

The NM_006645.3(STARD10):c.542G>A (p.Cys181Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain Significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: STARD10 NM_006645.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.36
• Publications: 0 publications found

Genes affected

STARD10 (HGNC:10666): (StAR related lipid transfer domain containing 10) Predicted to enable lipid carrier activity and phosphatidylcholine binding activity. Predicted to be involved in phosphatidylcholine biosynthetic process. 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, Jun 2026]

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]

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.

Variant Effect in Transcripts

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

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	STARD10 NM_006645.3	MANE Select	c.542G>A p.Cys181Tyr	missense	Exon 5 of 7	Prot: NP_006636.2 UniProt:

STARD10 NM_006645.3

MANE Select

HGVSc / HGVSpc.542G>Ap.Cys181Tyr

Exon rankExon 5 of 7

missense

Prot: NP_006636.2UniProt: Q9Y365

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	STARD10 ENST00000334805.11	TSL:1MANE Select	c.542G>A p.Cys181Tyr	missense	Exon 5 of 7	Prot: ENSP00000335247.6 UniProt:
	STARD10 ENST00000543304.5	TSL:1	c.542G>A p.Cys181Tyr	missense	Exon 6 of 8	Prot: ENSP00000438792.1 UniProt:
	STARD10 ENST00000538536.5	TSL:1	c.404G>A p.Cys135Tyr	missense	Exon 5 of 7	Prot: ENSP00000440016.1 UniProt:

STARD10 ENST00000334805.11

TSL:1MANE Select

HGVSc / HGVSpc.542G>Ap.Cys181Tyr

Exon rankExon 5 of 7

missense

Prot: ENSP00000335247.6UniProt: Q9Y365

STARD10 ENST00000543304.5

TSL:1

HGVSc / HGVSpc.542G>Ap.Cys181Tyr

Exon rankExon 6 of 8

missense

Prot: ENSP00000438792.1UniProt: Q9Y365

STARD10 ENST00000538536.5

TSL:1

HGVSc / HGVSpc.404G>Ap.Cys135Tyr

Exon rankExon 5 of 7

missense

Prot: ENSP00000440016.1UniProt: F5GY11

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 5 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33
TOPMed (Bravo)	AF: 0.00000378	AC:1	Hom:0	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.00	AC:0	Hom:0	AN:13470	Cov:

Showing 5 sources

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	31
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.28
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.43	T
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Uncertain	0.94	D
FuncVEP CTI	Pathogenic	0.98
GPN-Star LLR	N/A	-8.0
GPN-Star score	N/A	8.0
LIST_S2	Uncertain	0.93	D
M_CAP	Uncertain	0.18	D
MetaRNN	Pathogenic	0.91	D
MetaSVM	Uncertain	0.15	D
Mutation Taster	N/A	67/33	polymorphism
PhyloP100	Benign	3.4
popEVE	Benign	-4.0
PrimateAI	Uncertain	0.79	T
PromoterAI	N/A	-0.0010	Neutral
PROVEAN	Pathogenic	-8.8	D
REVEL	Uncertain	0.64
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0020	D
Varity_R	N/A	0.93
VESM-3B	Benign	-13

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs1858663557;

hg19: chr11-72468847;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar