chrX-101277652-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001168474.2(TAF7L):c.645G>T(p.Leu215Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000566 in 1,200,940 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001168474.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAF7L | ENST00000356784.2 | c.645G>T | p.Leu215Phe | missense_variant | Exon 9 of 13 | 1 | NM_001168474.2 | ENSP00000349235.1 | ||
TAF7L | ENST00000372907.7 | c.903G>T | p.Leu301Phe | missense_variant | Exon 9 of 13 | 1 | ENSP00000361998.3 | |||
TAF7L | ENST00000324762.10 | c.645G>T | p.Leu215Phe | missense_variant | Exon 8 of 11 | 2 | ENSP00000320283.6 |
Frequencies
GnomAD3 genomes AF: 0.000221 AC: 24AN: 108781Hom.: 0 Cov.: 21 AF XY: 0.000161 AC XY: 5AN XY: 31105
GnomAD3 exomes AF: 0.0000463 AC: 8AN: 172913Hom.: 0 AF XY: 0.0000342 AC XY: 2AN XY: 58543
GnomAD4 exome AF: 0.0000403 AC: 44AN: 1092159Hom.: 0 Cov.: 29 AF XY: 0.0000390 AC XY: 14AN XY: 358623
GnomAD4 genome AF: 0.000221 AC: 24AN: 108781Hom.: 0 Cov.: 21 AF XY: 0.000161 AC XY: 5AN XY: 31105
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.903G>T (p.L301F) alteration is located in exon 9 (coding exon 9) of the TAF7L gene. This alteration results from a G to T substitution at nucleotide position 903, causing the leucine (L) at amino acid position 301 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at