chr20-62006688-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003185.4(TAF4):c.2045C>A(p.Pro682Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,591,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003185.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAF4 | NM_003185.4 | c.2045C>A | p.Pro682Gln | missense_variant | 7/15 | ENST00000252996.9 | |
TAF4 | XM_047440429.1 | c.929C>A | p.Pro310Gln | missense_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF4 | ENST00000252996.9 | c.2045C>A | p.Pro682Gln | missense_variant | 7/15 | 1 | NM_003185.4 | P1 | |
TAF4 | ENST00000488539.1 | c.86C>A | p.Pro29Gln | missense_variant | 2/5 | 5 | |||
TAF4 | ENST00000436129.2 | n.416C>A | non_coding_transcript_exon_variant | 3/11 | 2 | ||||
TAF4 | ENST00000609041.1 | n.308C>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000678 AC: 16AN: 235894Hom.: 0 AF XY: 0.0000388 AC XY: 5AN XY: 128864
GnomAD4 exome AF: 0.0000125 AC: 18AN: 1439718Hom.: 0 Cov.: 30 AF XY: 0.00000840 AC XY: 6AN XY: 714284
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at