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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001940.4(ATN1):c.1479_1508del(p.Gln493_Gln502del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000369 in 1,584,052 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. Q488Q) has been classified as Likely benign.
Frequency
Consequence
NM_001940.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATN1 | NM_001940.4 | c.1479_1508del | p.Gln493_Gln502del | inframe_deletion | 5/10 | ENST00000396684.3 | |
ATN1 | NM_001007026.2 | c.1479_1508del | p.Gln493_Gln502del | inframe_deletion | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.1479_1508del | p.Gln493_Gln502del | inframe_deletion | 5/10 | 1 | NM_001940.4 | P1 | |
ATN1 | ENST00000356654.8 | c.1479_1508del | p.Gln493_Gln502del | inframe_deletion | 5/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000365 AC: 53AN: 145034Hom.: 0 Cov.: 0
GnomAD4 exome AF: 0.000370 AC: 532AN: 1438918Hom.: 0 AF XY: 0.000384 AC XY: 275AN XY: 716732
GnomAD4 genome ? AF: 0.000365 AC: 53AN: 145134Hom.: 0 Cov.: 0 AF XY: 0.000298 AC XY: 21AN XY: 70474
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at