12-6934581-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001940.4(ATN1):c.279+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000279 in 1,551,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001940.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.279+3G>A | splice_region_variant, intron_variant | Intron 4 of 9 | 1 | NM_001940.4 | ENSP00000379915.2 | |||
ATN1 | ENST00000356654.8 | c.279+3G>A | splice_region_variant, intron_variant | Intron 4 of 9 | 1 | ENSP00000349076.3 |
Frequencies
GnomAD3 genomes AF: 0.00126 AC: 192AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000399 AC: 65AN: 162934Hom.: 0 AF XY: 0.000293 AC XY: 25AN XY: 85468
GnomAD4 exome AF: 0.000173 AC: 242AN: 1399660Hom.: 0 Cov.: 29 AF XY: 0.000162 AC XY: 112AN XY: 691194
GnomAD4 genome AF: 0.00125 AC: 191AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at