rs9972882

Variant names:

• chr17-39651445-A-C
• rs9972882
• NM_006804.4:c.-51-2036A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-39651445-A-C
• chr17-39651445-A-G
• chr17-39651445-A-T

Variant summary

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

The NM_006804.4(STARD3):​c.-51-2036A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,010 control chromosomes in the GnomAD database, including 33,928 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 0.66 (33928 hom., cov: 32)
• Consequence: STARD3 NM_006804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 35 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD3	NM_006804.4	c.-51-2036A>C		intron_variant	Intron 1 of 14	ENST00000336308.10	NP_006795.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD3	ENST00000336308.10	c.-51-2036A>C		intron_variant	Intron 1 of 14	1	NM_006804.4	ENSP00000337446.5

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100323 AN: 151892 Hom.: 33898 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.661 AC: 100418 AN: 152010 Hom.: 33928 Cov.: 32 AF XY: 0.659 AC XY: 48945 AN XY: 74278

African (AFR) AF: 0.540 AC: 22332 AN: 41390

American (AMR) AF: 0.613 AC: 9360 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2462 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2176 AN: 5164

South Asian (SAS) AF: 0.749 AC: 3617 AN: 4830

European-Finnish (FIN) AF: 0.762 AC: 8062 AN: 10576

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50075 AN: 67986

Other (OTH) AF: 0.662 AC: 1399 AN: 2114

Alfa AF: 0.710 Hom.: 103711

Bravo AF: 0.642

Asia WGS AF: 0.654 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		-0.64
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: rs9972882; hg19: chr17-37807698;