12-6936728-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAG
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001940.4(ATN1):c.1494_1508delGCAGCAGCAGCAGCA(p.Gln498_Gln502del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.112 in 1,583,772 control chromosomes in the GnomAD database, including 7,674 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001940.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.1494_1508delGCAGCAGCAGCAGCA | p.Gln498_Gln502del | disruptive_inframe_deletion | Exon 5 of 10 | 1 | NM_001940.4 | ENSP00000379915.2 | ||
ATN1 | ENST00000356654.8 | c.1494_1508delGCAGCAGCAGCAGCA | p.Gln498_Gln502del | disruptive_inframe_deletion | Exon 5 of 10 | 1 | ENSP00000349076.3 |
Frequencies
GnomAD3 genomes AF: 0.0951 AC: 13793AN: 144976Hom.: 869 Cov.: 0
GnomAD4 exome AF: 0.113 AC: 163219AN: 1438696Hom.: 6803 AF XY: 0.111 AC XY: 79674AN XY: 716618
GnomAD4 genome AF: 0.0951 AC: 13791AN: 145076Hom.: 871 Cov.: 0 AF XY: 0.0957 AC XY: 6743AN XY: 70440
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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The ATN1 p.Gln498_Gln502del variant was not identified in the literature nor was it identified in the MutDB or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs377147612), ClinVar and Cosmic. The variant was identified in control databases in 41 of 259998 chromosomes at a frequency of 0.000158 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 19 of 20928 chromosomes (freq: 0.000908), Other in 2 of 6794 chromosomes (freq: 0.000294), Latino in 9 of 31612 chromosomes (freq: 0.000285), East Asian in 3 of 16812 chromosomes (freq: 0.000178) and European (non-Finnish) in 8 of 122724 chromosomes (freq: 0.000065), while the variant was not observed in the Ashkenazi Jewish, European (Finnish) and South Asian populations. This variant is an in-frame deletion resulting in the removal of 5 glutamine (gln) residues at codon 498, within a glutamine repeat region. The insertion of (CAG)n or glutamine repeats has been found to cause dentatorubro-pallidoluysian atrophy, however this variant is a (CAG)n repeat deletion within the normal range of 6-35 repeats (Koide_1994_PMID: 8136840; MIM: 607462). The impact of this alteration on ATN1 protein function is not known, however MutationTaster predicts this variant to be a polymorphism. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at