20-3471204-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_139321.3(ATRN):āc.97T>Cā(p.Trp33Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_139321.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRN | NM_139321.3 | c.97T>C | p.Trp33Arg | missense_variant | 1/29 | ENST00000262919.10 | |
ATRN | NM_001323332.2 | c.97T>C | p.Trp33Arg | missense_variant | 1/26 | ||
ATRN | NM_139322.4 | c.97T>C | p.Trp33Arg | missense_variant | 1/25 | ||
ATRN | NM_001207047.3 | c.62+70T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRN | ENST00000262919.10 | c.97T>C | p.Trp33Arg | missense_variant | 1/29 | 5 | NM_139321.3 | P2 | |
ATRN | ENST00000446916.2 | c.97T>C | p.Trp33Arg | missense_variant | 1/25 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152032Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1347958Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 664462
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152032Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 10, 2023 | The c.97T>C (p.W33R) alteration is located in exon 1 (coding exon 1) of the ATRN gene. This alteration results from a T to C substitution at nucleotide position 97, causing the tryptophan (W) at amino acid position 33 to be replaced by an arginine (R). 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