chr9-15187012-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_152574.3(TTC39B):c.1221A>G(p.Ala407=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,613,210 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0065 ( 10 hom., cov: 33)
Exomes 𝑓: 0.00065 ( 10 hom. )
Consequence
TTC39B
NM_152574.3 synonymous
NM_152574.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0700
Genes affected
TTC39B (HGNC:23704): (tetratricopeptide repeat domain 39B) Predicted to be involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.51).
BP6
?
Variant 9-15187012-T-C is Benign according to our data. Variant chr9-15187012-T-C is described in ClinVar as [Benign]. Clinvar id is 776411.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.07 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00645 (983/152328) while in subpopulation AFR AF= 0.0223 (926/41576). AF 95% confidence interval is 0.0211. There are 10 homozygotes in gnomad4. There are 480 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC39B | NM_152574.3 | c.1221A>G | p.Ala407= | synonymous_variant | 15/20 | ENST00000512701.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC39B | ENST00000512701.7 | c.1221A>G | p.Ala407= | synonymous_variant | 15/20 | 2 | NM_152574.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00642 AC: 977AN: 152210Hom.: 10 Cov.: 33
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GnomAD3 exomes AF: 0.00158 AC: 395AN: 250254Hom.: 3 AF XY: 0.00115 AC XY: 155AN XY: 135262
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GnomAD4 exome AF: 0.000648 AC: 947AN: 1460882Hom.: 10 Cov.: 30 AF XY: 0.000566 AC XY: 411AN XY: 726728
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GnomAD4 genome ? AF: 0.00645 AC: 983AN: 152328Hom.: 10 Cov.: 33 AF XY: 0.00644 AC XY: 480AN XY: 74494
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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 30, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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