12-6934472-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001940.4(ATN1):c.173G>A(p.Arg58Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00001 in 1,592,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001940.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 6AN: 215182Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 115682
GnomAD4 exome AF: 0.00000972 AC: 14AN: 1440592Hom.: 0 Cov.: 31 AF XY: 0.00000979 AC XY: 7AN XY: 714798
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74268
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.173G>A (p.R58Q) alteration is located in exon 4 (coding exon 3) of the ATN1 gene. This alteration results from a G to A substitution at nucleotide position 173, causing the arginine (R) at amino acid position 58 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at