rs5951328
Positions:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The ENST00000372907.7(TAF7L):āc.101T>Cā(p.Leu34Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: š 0.99 ( 38178 hom., 30539 hem., cov: 21)
Exomes š: 0.99 ( 356626 hom. 358515 hem. )
Failed GnomAD Quality Control
Consequence
TAF7L
ENST00000372907.7 missense
ENST00000372907.7 missense
Scores
16
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.28
Genes affected
TAF7L (HGNC:11548): (TATA-box binding protein associated factor 7 like) This gene is similar to a mouse gene that encodes a TATA box binding protein-associated factor, and shows testis-specific expression. The encoded protein could be a spermatogenesis-specific component of the DNA-binding general transcription factor complex TFIID. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.402261E-6).
BP6
?
Variant X-101292945-A-G is Benign according to our data. Variant chrX-101292945-A-G is described in Lovd as [Benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAF7L | NM_024885.4 | c.101T>C | p.Leu34Pro | missense_variant | 1/13 | ||
TAF7L | XM_006724664.2 | c.101T>C | p.Leu34Pro | missense_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF7L | ENST00000372907.7 | c.101T>C | p.Leu34Pro | missense_variant | 1/13 | 1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 107526AN: 108494Hom.: 38182 Cov.: 21 AF XY: 0.992 AC XY: 30473AN XY: 30732 FAILED QC
GnomAD3 genomes
?
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FAILED QC
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GnomAD3 exomes AF: 0.991 AC: 181518AN: 183187Hom.: 56665 AF XY: 0.991 AC XY: 67158AN XY: 67773
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.986 AC: 1082358AN: 1098208Hom.: 356626 Cov.: 59 AF XY: 0.986 AC XY: 358515AN XY: 363570
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.991 AC: 107583AN: 108550Hom.: 38178 Cov.: 21 AF XY: 0.992 AC XY: 30539AN XY: 30798
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Data not reliable, filtered out with message: InbreedingCoeff
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2829
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MPC
ClinPred
T
GERP RS
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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