rs3817160

Variant names:

• chr17-39637562-C-G
• rs3817160
• NM_006804.4:c.-52+331C>G

Your query was ambiguous. Multiple possible variants found:

• chr17-39637562-C-G
• chr17-39637562-C-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.-52+331C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,956 control chromosomes in the GnomAD database, including 31,598 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 0.61 (31582 hom., cov: 30)
  • Exomes 𝑓: 0.84 (16 hom.)
• Consequence: STARD3 NM_006804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457
• Publications: 15 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD3	NM_006804.4	MANE Select	c.-52+331C>G		intron	N/A	NP_006795.3
	STARD3	NM_001165937.2		c.-52+331C>G		intron	N/A	NP_001159409.1	Q14849-3
	STARD3	NM_001165938.2		c.-52+331C>G		intron	N/A	NP_001159410.1	Q14849-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STARD3	ENST00000336308.10	TSL:1 MANE Select	c.-52+331C>G		intron	N/A	ENSP00000337446.5	Q14849-1
	STARD3	ENST00000580611.5	TSL:5	c.-52+331C>G		intron	N/A	ENSP00000463613.1	J3QLM1
	STARD3	ENST00000936728.1		c.-52+331C>G		intron	N/A	ENSP00000606787.1

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92387 AN: 151794 Hom.: 31575 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.640

GnomAD4 exome AF: 0.841 AC: 37 AN: 44 Hom.: 16 Cov.: 0 AF XY: 0.833 AC XY: 25 AN XY: 30

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.929 AC: 13 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.875 AC: 14 AN: 16

Other (OTH) AF: 0.900 AC: 9 AN: 10

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0342046), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.608 AC: 92417 AN: 151912 Hom.: 31582 Cov.: 30 AF XY: 0.608 AC XY: 45128 AN XY: 74248

African (AFR) AF: 0.291 AC: 12025 AN: 41366

American (AMR) AF: 0.615 AC: 9391 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2560 AN: 3466

East Asian (EAS) AF: 0.440 AC: 2270 AN: 5154

South Asian (SAS) AF: 0.722 AC: 3481 AN: 4818

European-Finnish (FIN) AF: 0.779 AC: 8228 AN: 10566

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52224 AN: 67958

Other (OTH) AF: 0.640 AC: 1348 AN: 2106

Alfa AF: 0.564 Hom.: 1909

Bravo AF: 0.581

Asia WGS AF: 0.606 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		0.46
PromoterAI		-0.040	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3817160; hg19: chr17-37793815; COSMIC: COSV54201774; COSMIC: COSV54201774;