chr12-6936728-ACAG-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001940.4(ATN1):c.1506_1508delGCA(p.Gln502del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 1,548,102 control chromosomes in the GnomAD database, including 569 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001940.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.1506_1508delGCA | p.Gln502del | disruptive_inframe_deletion | Exon 5 of 10 | 1 | NM_001940.4 | ENSP00000379915.2 | ||
ATN1 | ENST00000356654.8 | c.1506_1508delGCA | p.Gln502del | disruptive_inframe_deletion | Exon 5 of 10 | 1 | ENSP00000349076.3 |
Frequencies
GnomAD3 genomes AF: 0.0419 AC: 6069AN: 144946Hom.: 152 Cov.: 0
GnomAD4 exome AF: 0.0455 AC: 63789AN: 1403058Hom.: 418 AF XY: 0.0472 AC XY: 32931AN XY: 698220
GnomAD4 genome AF: 0.0419 AC: 6073AN: 145044Hom.: 151 Cov.: 0 AF XY: 0.0406 AC XY: 2862AN XY: 70440
ClinVar
Submissions by phenotype
not specified Benign:1
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not provided Benign:1
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Dentatorubral-pallidoluysian atrophy;C5193125:Congenital hypotonia, epilepsy, developmental delay, and digital anomalies Benign:1
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ATN1-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