chr22-39381844-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004711.5(SYNGR1):āc.632G>Cā(p.Gly211Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000036 in 1,612,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G211V) has been classified as Uncertain significance.
Frequency
Consequence
NM_004711.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNGR1 | NM_004711.5 | c.632G>C | p.Gly211Ala | missense_variant | 4/4 | ENST00000328933.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNGR1 | ENST00000328933.10 | c.632G>C | p.Gly211Ala | missense_variant | 4/4 | 1 | NM_004711.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000683 AC: 17AN: 249034Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135258
GnomAD4 exome AF: 0.0000377 AC: 55AN: 1460688Hom.: 0 Cov.: 35 AF XY: 0.0000413 AC XY: 30AN XY: 726680
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2023 | The c.632G>C (p.G211A) alteration is located in exon 4 (coding exon 4) of the SYNGR1 gene. This alteration results from a G to C substitution at nucleotide position 632, causing the glycine (G) at amino acid position 211 to be replaced by an alanine (A). 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