15-81309441-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000302824.7(STARD5):c.*3815A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,618 control chromosomes in the GnomAD database, including 8,026 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.32 ( 7995 hom., cov: 33)
Exomes 𝑓: 0.33 ( 31 hom. )
Consequence
STARD5
ENST00000302824.7 3_prime_UTR
ENST00000302824.7 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.375
Genes affected
IL16 (HGNC:5980): (interleukin 16) The protein encoded by this gene is a pleiotropic cytokine that functions as a chemoattractant, a modulator of T cell activation, and an inhibitor of HIV replication. The signaling process of this cytokine is mediated by CD4. The product of this gene undergoes proteolytic processing, which is found to yield two functional proteins. The cytokine function is exclusively attributed to the secreted C-terminal peptide, while the N-terminal product may play a role in cell cycle control. Caspase 3 is reported to be involved in the proteolytic processing of this protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
STARD5 (HGNC:18065): (StAR related lipid transfer domain containing 5) Proteins containing a steroidogenic acute regulatory-related lipid transfer (START) domain are often involved in the trafficking of lipids and cholesterol between diverse intracellular membranes. This gene is a member of the StarD subfamily that encodes START-related lipid transfer proteins. The protein encoded by this gene is a cholesterol transporter and is also able to bind and transport other sterol-derived molecules related to the cholesterol/bile acid biosynthetic pathways such as 25-hydroxycholesterol. Its expression is upregulated during endoplasmic reticulum (ER) stress. The protein is thought to act as a cytosolic sterol transporter that moves cholesterol between intracellular membranes such as from the cytoplasm to the ER and from the ER to the Golgi apparatus. Alternative splicing of this gene produces multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 15-81309441-T-C is Benign according to our data. Variant chr15-81309441-T-C is described in ClinVar as [Benign]. Clinvar id is 1261119.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL16 | NM_172217.5 | c.*643T>C | 3_prime_UTR_variant | 19/19 | ENST00000683961.1 | NP_757366.2 | ||
STARD5 | NM_181900.3 | c.*3815A>G | 3_prime_UTR_variant | 6/6 | ENST00000302824.7 | NP_871629.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STARD5 | ENST00000302824.7 | c.*3815A>G | 3_prime_UTR_variant | 6/6 | 1 | NM_181900.3 | ENSP00000304032 | P1 | ||
IL16 | ENST00000683961.1 | c.*643T>C | 3_prime_UTR_variant | 19/19 | NM_172217.5 | ENSP00000508085 | A2 | |||
ENST00000607019.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.322 AC: 48992AN: 151996Hom.: 7984 Cov.: 33
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GnomAD4 exome AF: 0.329 AC: 165AN: 502Hom.: 31 Cov.: 0 AF XY: 0.317 AC XY: 90AN XY: 284
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GnomAD4 genome AF: 0.322 AC: 49045AN: 152116Hom.: 7995 Cov.: 33 AF XY: 0.318 AC XY: 23630AN XY: 74376
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2020 | This variant is associated with the following publications: (PMID: 24465869) - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at