17-39648605-T-C

Variant names:

• chr17-39648605-T-C
• rs9892427
• NM_006804.4:c.-51-4876T>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.-51-4876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,148 control chromosomes in the GnomAD database, including 2,069 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 0.13 (2069 hom., cov: 31)
• Consequence: STARD3 NM_006804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 10 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006804.4. 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
	STARD3	NM_006804.4	MANE Select	c.-51-4876T>C		intron	N/A	NP_006795.3
	STARD3	NM_001165937.2		c.-51-4876T>C		intron	N/A	NP_001159409.1
	STARD3	NM_001165938.2		c.-51-4876T>C		intron	N/A	NP_001159410.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD3	ENST00000336308.10	TSL:1 MANE Select	c.-51-4876T>C		intron	N/A	ENSP00000337446.5
	STARD3	ENST00000580611.5	TSL:5	c.-51-4876T>C		intron	N/A	ENSP00000463613.1
	STARD3	ENST00000544210.6	TSL:2	c.-51-4876T>C		intron	N/A	ENSP00000439869.2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19813 AN: 152030 Hom.: 2059 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0434

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.131 AC: 19873 AN: 152148 Hom.: 2069 Cov.: 31 AF XY: 0.127 AC XY: 9449 AN XY: 74396

African (AFR) AF: 0.290 AC: 12017 AN: 41452

American (AMR) AF: 0.0712 AC: 1089 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5180

South Asian (SAS) AF: 0.0428 AC: 206 AN: 4816

European-Finnish (FIN) AF: 0.0702 AC: 746 AN: 10622

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5409 AN: 67990

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0898 Hom.: 1509

Bravo AF: 0.138

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.15
DANN	Benign	0.75
PhyloP100		-0.12
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: rs9892427; hg19: chr17-37804858;