7-73708629-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_004603.4(STX1A):c.168G>A(p.Arg56Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,810 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_004603.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STX1A | NM_004603.4 | c.168G>A | p.Arg56Arg | synonymous_variant | Exon 3 of 10 | ENST00000222812.8 | NP_004594.1 | |
STX1A | NM_001165903.2 | c.168G>A | p.Arg56Arg | synonymous_variant | Exon 3 of 10 | NP_001159375.1 | ||
STX1A | XM_047420777.1 | c.168G>A | p.Arg56Arg | synonymous_variant | Exon 3 of 9 | XP_047276733.1 | ||
STX1A | XM_047420778.1 | c.168G>A | p.Arg56Arg | synonymous_variant | Exon 3 of 9 | XP_047276734.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461810Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727200
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
STX1A: PM2:Supporting, BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.