chr13-33112903-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_178006.4(STARD13):c.2310C>T(p.Ala770=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000937 in 1,612,082 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00055 ( 4 hom. )
Consequence
STARD13
NM_178006.4 synonymous
NM_178006.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.77
Genes affected
STARD13 (HGNC:19164): (StAR related lipid transfer domain containing 13) This gene encodes a protein which contains an N-terminal sterile alpha motif (SAM) for protein-protein interactions, followed by an ATP/GTP-binding motif, a GTPase-activating protein (GAP) domain, and a C-terminal STAR-related lipid transfer (START) domain. It may be involved in regulation of cytoskeletal reorganization, cell proliferation, and cell motility, and acts as a tumor suppressor in hepatoma cells. The gene is located in a region of chromosome 13 that is associated with loss of heterozygosity in hepatocellular carcinomas. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 13-33112903-G-A is Benign according to our data. Variant chr13-33112903-G-A is described in ClinVar as [Benign]. Clinvar id is 726916.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.77 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000549 (802/1459740) while in subpopulation AFR AF= 0.0166 (554/33394). AF 95% confidence interval is 0.0154. There are 4 homozygotes in gnomad4_exome. There are 331 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STARD13 | NM_178006.4 | c.2310C>T | p.Ala770= | synonymous_variant | 9/14 | ENST00000336934.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STARD13 | ENST00000336934.10 | c.2310C>T | p.Ala770= | synonymous_variant | 9/14 | 1 | NM_178006.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00466 AC: 710AN: 152224Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00126 AC: 311AN: 247458Hom.: 0 AF XY: 0.000828 AC XY: 111AN XY: 134094
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GnomAD4 exome AF: 0.000549 AC: 802AN: 1459740Hom.: 4 Cov.: 31 AF XY: 0.000456 AC XY: 331AN XY: 726038
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GnomAD4 genome AF: 0.00465 AC: 709AN: 152342Hom.: 10 Cov.: 32 AF XY: 0.00444 AC XY: 331AN XY: 74492
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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 submitter | clinical testing | Invitae | Apr 09, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at