19-2981572-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001143986.2(TLE6):āc.169A>Gā(p.Ile57Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000516 in 1,551,264 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001143986.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLE6 | NM_001143986.2 | c.169A>G | p.Ile57Val | missense_variant | 4/17 | ENST00000246112.9 | |
TLE6 | XM_005259645.3 | c.169A>G | p.Ile57Val | missense_variant | 4/17 | ||
TLE6 | XM_011528300.3 | c.169A>G | p.Ile57Val | missense_variant | 4/17 | ||
TLE6 | NM_024760.3 | c.-201A>G | 5_prime_UTR_variant | 3/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLE6 | ENST00000246112.9 | c.169A>G | p.Ile57Val | missense_variant | 4/17 | 1 | NM_001143986.2 | A2 | |
TLE6 | ENST00000452088.5 | c.-201A>G | 5_prime_UTR_variant | 3/16 | 1 | P2 | |||
TLE6 | ENST00000453329.5 | c.169A>G | p.Ile57Val | missense_variant | 4/7 | 4 | |||
TLE6 | ENST00000468176.7 | n.252A>G | non_coding_transcript_exon_variant | 4/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151896Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000500 AC: 7AN: 1399368Hom.: 0 Cov.: 32 AF XY: 0.00000435 AC XY: 3AN XY: 690190
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151896Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74178
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at