chrX-47574692-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006950.3(SYN1):āc.1389A>Gā(p.Pro463=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,069,198 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P463P) has been classified as Likely benign.
Frequency
Consequence
NM_006950.3 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 |
---|---|---|---|---|---|---|---|
SYN1 | NM_006950.3 | c.1389A>G | p.Pro463= | synonymous_variant | 11/13 | ENST00000295987.13 | |
SYN1 | NM_133499.2 | c.1389A>G | p.Pro463= | synonymous_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYN1 | ENST00000295987.13 | c.1389A>G | p.Pro463= | synonymous_variant | 11/13 | 2 | NM_006950.3 | P3 | |
SYN1 | ENST00000340666.5 | c.1389A>G | p.Pro463= | synonymous_variant | 11/13 | 1 | A1 | ||
SYN1 | ENST00000640721.1 | c.66A>G | p.Pro22= | synonymous_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000801 AC: 1AN: 124839Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 40099
GnomAD4 exome AF: 0.00000187 AC: 2AN: 1069198Hom.: 0 Cov.: 31 AF XY: 0.00000288 AC XY: 1AN XY: 347784
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at