ENST00000354777.6:c.1554delT
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The ENST00000354777.6(WLS):c.1554delT(p.Phe518LeufsTer65) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000389 in 1,613,720 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000354777.6 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WLS | NM_001002292.4 | c.1554delT | p.Phe518LeufsTer65 | frameshift_variant | Exon 12 of 12 | NP_001002292.3 | ||
WLS | XM_011542191.3 | c.1560delT | p.Phe520LeufsTer65 | frameshift_variant | Exon 12 of 12 | XP_011540493.1 | ||
GNG12-AS1 | NR_040077.1 | n.410delA | non_coding_transcript_exon_variant | Exon 4 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WLS | ENST00000354777.6 | c.1554delT | p.Phe518LeufsTer65 | frameshift_variant | Exon 12 of 12 | 1 | ENSP00000346829.2 | |||
GNG12-AS1 | ENST00000413628.5 | n.379delA | non_coding_transcript_exon_variant | Exon 4 of 9 | 2 | |||||
GNG12-AS1 | ENST00000420587.5 | n.395delA | non_coding_transcript_exon_variant | Exon 4 of 10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152150Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000800 AC: 199AN: 248610Hom.: 2 AF XY: 0.00103 AC XY: 138AN XY: 134558
GnomAD4 exome AF: 0.000406 AC: 594AN: 1461452Hom.: 5 Cov.: 30 AF XY: 0.000553 AC XY: 402AN XY: 727024
GnomAD4 genome AF: 0.000223 AC: 34AN: 152268Hom.: 3 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
- -
WLS-related disorder Benign:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at