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GeneBe

17-39658771-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_006804.4(STARD3):c.597C>T(p.Ser199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 1,614,032 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0051 ( 55 hom. )

Consequence

STARD3
NM_006804.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.96
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-39658771-C-T is Benign according to our data. Variant chr17-39658771-C-T is described in ClinVar as [Benign]. Clinvar id is 2647719.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.96 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00513 (7499/1461808) while in subpopulation MID AF= 0.0258 (149/5768). AF 95% confidence interval is 0.0225. There are 55 homozygotes in gnomad4_exome. There are 4095 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STARD3NM_006804.4 linkuse as main transcriptc.597C>T p.Ser199= synonymous_variant 7/15 ENST00000336308.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STARD3ENST00000336308.10 linkuse as main transcriptc.597C>T p.Ser199= synonymous_variant 7/151 NM_006804.4 P1Q14849-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00415
AC:
632
AN:
152106
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00229
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00570
Gnomad ASJ
AF:
0.00432
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0166
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.00485
Gnomad OTH
AF:
0.00766
GnomAD3 exomes
AF:
0.00617
AC:
1551
AN:
251326
Hom.:
11
AF XY:
0.00701
AC XY:
952
AN XY:
135856
show subpopulations
Gnomad AFR exome
AF:
0.00203
Gnomad AMR exome
AF:
0.00521
Gnomad ASJ exome
AF:
0.00447
Gnomad EAS exome
AF:
0.000381
Gnomad SAS exome
AF:
0.0184
Gnomad FIN exome
AF:
0.000139
Gnomad NFE exome
AF:
0.00588
Gnomad OTH exome
AF:
0.00847
GnomAD4 exome
AF:
0.00513
AC:
7499
AN:
1461808
Hom.:
55
Cov.:
32
AF XY:
0.00563
AC XY:
4095
AN XY:
727218
show subpopulations
Gnomad4 AFR exome
AF:
0.00179
Gnomad4 AMR exome
AF:
0.00550
Gnomad4 ASJ exome
AF:
0.00509
Gnomad4 EAS exome
AF:
0.000202
Gnomad4 SAS exome
AF:
0.0182
Gnomad4 FIN exome
AF:
0.000394
Gnomad4 NFE exome
AF:
0.00439
Gnomad4 OTH exome
AF:
0.00714
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00415
AC:
632
AN:
152224
Hom.:
2
Cov.:
33
AF XY:
0.00407
AC XY:
303
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.00229
Gnomad4 AMR
AF:
0.00569
Gnomad4 ASJ
AF:
0.00432
Gnomad4 EAS
AF:
0.000194
Gnomad4 SAS
AF:
0.0166
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.00485
Gnomad4 OTH
AF:
0.00758
Alfa
AF:
0.00491
Hom.:
1
Bravo
AF:
0.00451
Asia WGS
AF:
0.00693
AC:
24
AN:
3478
EpiCase
AF:
0.00665
EpiControl
AF:
0.00806

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2023STARD3: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
Cadd
Benign
1.6
Dann
Benign
0.57
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs142935105; hg19: chr17-37815024; COSMIC: COSV60421159; COSMIC: COSV60421159; API