chr12-6939123-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_001940.4(ATN1):c.3160C>A(p.His1054Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H1054Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001940.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.3160C>A | p.His1054Asn | missense_variant | Exon 7 of 10 | 1 | NM_001940.4 | ENSP00000379915.2 | ||
ATN1 | ENST00000356654.8 | c.3160C>A | p.His1054Asn | missense_variant | Exon 7 of 10 | 1 | ENSP00000349076.3 | |||
ATN1 | ENST00000537488.1 | n.17C>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 | |||||
ATN1 | ENST00000541029.1 | n.*158C>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Congenital ATN1 related disorder Pathogenic:1
affected individual has clinical features consistent with congenital ATN1 related disorder -
Congenital hypotonia, epilepsy, developmental delay, and digital anomalies Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at