chr20-3471293-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_139321.3(ATRN):c.186G>A(p.Leu62=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000756 in 1,323,412 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 Likely benign (★).
Frequency
Consequence
NM_139321.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRN | NM_139321.3 | c.186G>A | p.Leu62= | synonymous_variant | 1/29 | ENST00000262919.10 | |
ATRN | NM_001323332.2 | c.186G>A | p.Leu62= | synonymous_variant | 1/26 | ||
ATRN | NM_139322.4 | c.186G>A | p.Leu62= | synonymous_variant | 1/25 | ||
ATRN | NM_001207047.3 | c.62+159G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRN | ENST00000262919.10 | c.186G>A | p.Leu62= | synonymous_variant | 1/29 | 5 | NM_139321.3 | P2 | |
ATRN | ENST00000446916.2 | c.186G>A | p.Leu62= | synonymous_variant | 1/25 | 1 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.56e-7 AC: 1AN: 1323412Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 651954
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.