chr10-127175698-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039762.3(INSYN2A):c.698G>A(p.Gly233Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039762.3 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 |
---|---|---|---|---|---|---|---|
INSYN2A | NM_001039762.3 | c.698G>A | p.Gly233Glu | missense_variant | 4/6 | ENST00000522781.6 | |
DOCK1 | NM_001290223.2 | c.2847+47934C>T | intron_variant | ENST00000623213.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSYN2A | ENST00000522781.6 | c.698G>A | p.Gly233Glu | missense_variant | 4/6 | 2 | NM_001039762.3 | P1 | |
DOCK1 | ENST00000623213.2 | c.2847+47934C>T | intron_variant | 1 | NM_001290223.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249688Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135256
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461614Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 727110
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.698G>A (p.G233E) alteration is located in exon 4 (coding exon 1) of the FAM196A gene. This alteration results from a G to A substitution at nucleotide position 698, causing the glycine (G) at amino acid position 233 to be replaced by a glutamic acid (E). 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