chr17-39657603-G-C

Variant names:

• chr17-39657603-G-C
• rs11869286
• NM_006804.4:c.298-172G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006804.4(STARD3):​c.298-172G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,830 control chromosomes in the GnomAD database, including 23,959 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 0.53 (23959 hom., cov: 31)
• Consequence: STARD3 NM_006804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 103 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD3	NM_006804.4	c.298-172G>C		intron_variant	Intron 3 of 14	ENST00000336308.10	NP_006795.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD3	ENST00000336308.10	c.298-172G>C		intron_variant	Intron 3 of 14	1	NM_006804.4	ENSP00000337446.5

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80310 AN: 151716 Hom.: 23951 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.529 AC: 80342 AN: 151830 Hom.: 23959 Cov.: 31 AF XY: 0.531 AC XY: 39395 AN XY: 74210

African (AFR) AF: 0.248 AC: 10262 AN: 41384

American (AMR) AF: 0.541 AC: 8267 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2371 AN: 3472

East Asian (EAS) AF: 0.415 AC: 2138 AN: 5156

South Asian (SAS) AF: 0.705 AC: 3396 AN: 4814

European-Finnish (FIN) AF: 0.692 AC: 7279 AN: 10518

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44599 AN: 67902

Other (OTH) AF: 0.561 AC: 1180 AN: 2104

Alfa AF: 0.636 Hom.: 17480

Bravo AF: 0.503

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		-0.067
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: rs11869286; hg19: chr17-37813856;