17-39653965-C-G

Variant names:

• chr17-39653965-C-G
• rs881844
• NM_006804.4:c.219+215C>G

Variant summary

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

The NM_006804.4(STARD3):​c.219+215C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,082 control chromosomes in the GnomAD database, including 23,480 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 0.52 (23480 hom., cov: 32)
• Consequence: STARD3 NM_006804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 33 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD3	NM_006804.4	c.219+215C>G		intron_variant	Intron 2 of 14	ENST00000336308.10	NP_006795.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD3	ENST00000336308.10	c.219+215C>G		intron_variant	Intron 2 of 14	1	NM_006804.4	ENSP00000337446.5

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78938 AN: 151964 Hom.: 23473 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.519 AC: 78956 AN: 152082 Hom.: 23480 Cov.: 32 AF XY: 0.520 AC XY: 38689 AN XY: 74342

African (AFR) AF: 0.223 AC: 9232 AN: 41486

American (AMR) AF: 0.533 AC: 8134 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2309 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2118 AN: 5156

South Asian (SAS) AF: 0.699 AC: 3368 AN: 4820

European-Finnish (FIN) AF: 0.692 AC: 7322 AN: 10586

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44493 AN: 67972

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.459 Hom.: 1575

Bravo AF: 0.492

Asia WGS AF: 0.574 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-1.3
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: rs881844; hg19: chr17-37810218;