chrX-49193275-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_003179.3(SYP):c.612G>A(p.Ser204=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,210,533 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 49 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003179.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYP | NM_003179.3 | c.612G>A | p.Ser204= | synonymous_variant | 5/7 | ENST00000263233.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYP | ENST00000263233.9 | c.612G>A | p.Ser204= | synonymous_variant | 5/7 | 1 | NM_003179.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000683 AC: 77AN: 112815Hom.: 0 Cov.: 24 AF XY: 0.000687 AC XY: 24AN XY: 34953
GnomAD3 exomes AF: 0.000172 AC: 31AN: 180316Hom.: 0 AF XY: 0.0000612 AC XY: 4AN XY: 65326
GnomAD4 exome AF: 0.0000884 AC: 97AN: 1097664Hom.: 0 Cov.: 32 AF XY: 0.0000689 AC XY: 25AN XY: 363056
GnomAD4 genome ? AF: 0.000682 AC: 77AN: 112869Hom.: 0 Cov.: 24 AF XY: 0.000685 AC XY: 24AN XY: 35017
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 03, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at