chr17-35822714-A-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_139215.3(TAF15):c.365A>G(p.Tyr122Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000398 in 1,614,214 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 2 hom. )
Consequence
TAF15
NM_139215.3 missense
NM_139215.3 missense
Scores
3
8
5
Clinical Significance
Conservation
PhyloP100: 3.87
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009331882).
BP6
?
Variant 17-35822714-A-G is Benign according to our data. Variant chr17-35822714-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 730618.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 273 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAF15 | NM_139215.3 | c.365A>G | p.Tyr122Cys | missense_variant | 6/16 | ENST00000605844.6 | |
TAF15 | NM_003487.4 | c.356A>G | p.Tyr119Cys | missense_variant | 6/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF15 | ENST00000605844.6 | c.365A>G | p.Tyr122Cys | missense_variant | 6/16 | 1 | NM_139215.3 | P2 | |
ENST00000603678.1 | n.317-895A>G | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000603981.1 | n.264-5773T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00179 AC: 273AN: 152226Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000505 AC: 127AN: 251434Hom.: 1 AF XY: 0.000361 AC XY: 49AN XY: 135890
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GnomAD4 exome AF: 0.000254 AC: 371AN: 1461870Hom.: 2 Cov.: 31 AF XY: 0.000217 AC XY: 158AN XY: 727232
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2018 | - - |
TAF15-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 14, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;T;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;.;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;D;D;T;D
Polyphen
D;.;.;.;D
Vest4
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at