rs886039355
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_000127.3(EXT1):c.1466_1468del(p.Pro489del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,158 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P489P) has been classified as Likely benign.
Frequency
Consequence
NM_000127.3 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXT1 | NM_000127.3 | c.1466_1468del | p.Pro489del | inframe_deletion | 6/11 | ENST00000378204.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXT1 | ENST00000378204.7 | c.1466_1468del | p.Pro489del | inframe_deletion | 6/11 | 1 | NM_000127.3 | P1 | |
EXT1 | ENST00000684189.1 | n.933_935del | non_coding_transcript_exon_variant | 6/11 | |||||
EXT1 | ENST00000437196.1 | c.*357_*359del | 3_prime_UTR_variant, NMD_transcript_variant | 5/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at