17-35820316-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_139215.3(TAF15):c.185-16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000916 in 1,613,196 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0042 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00058 ( 1 hom. )
Consequence
TAF15
NM_139215.3 intron
NM_139215.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.518
Genes affected
TAF15 (HGNC:11547): (TATA-box binding protein associated factor 15) This gene encodes a member of the TET family of RNA-binding proteins. The encoded protein plays a role in RNA polymerase II gene transcription as a component of a distinct subset of multi-subunit transcription initiation factor TFIID complexes. Translocations involving this gene play a role in acute leukemia and extraskeletal myxoid chondrosarcoma, and mutations in this gene may play a role in amyotrophic lateral sclerosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 17-35820316-C-T is Benign according to our data. Variant chr17-35820316-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1300617.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000579 (846/1460954) while in subpopulation AFR AF= 0.0162 (541/33462). AF 95% confidence interval is 0.015. There are 1 homozygotes in gnomad4_exome. There are 393 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 632 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00413 AC: 628AN: 152124Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00117 AC: 295AN: 251284Hom.: 1 AF XY: 0.000854 AC XY: 116AN XY: 135828
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GnomAD4 exome AF: 0.000579 AC: 846AN: 1460954Hom.: 1 Cov.: 32 AF XY: 0.000541 AC XY: 393AN XY: 726836
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GnomAD4 genome AF: 0.00415 AC: 632AN: 152242Hom.: 3 Cov.: 32 AF XY: 0.00388 AC XY: 289AN XY: 74434
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 05, 2020 | - - |
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