chr5-169882757-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001129891.3(INSYN2B):c.1142C>T(p.Ser381Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,399,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S381T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001129891.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INSYN2B | NM_001129891.3 | c.1142C>T | p.Ser381Phe | missense_variant | 2/4 | ENST00000377365.4 | |
DOCK2 | NM_004946.3 | c.2799+41905G>A | intron_variant | ENST00000520908.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSYN2B | ENST00000377365.4 | c.1142C>T | p.Ser381Phe | missense_variant | 2/4 | 2 | NM_001129891.3 | P1 | |
DOCK2 | ENST00000520908.7 | c.2799+41905G>A | intron_variant | 2 | NM_004946.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000127 AC: 2AN: 157430Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83146
GnomAD4 exome AF: 0.0000136 AC: 19AN: 1399572Hom.: 0 Cov.: 32 AF XY: 0.0000101 AC XY: 7AN XY: 690284
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2022 | The c.1142C>T (p.S381F) alteration is located in exon 2 (coding exon 1) of the FAM196B gene. This alteration results from a C to T substitution at nucleotide position 1142, causing the serine (S) at amino acid position 381 to be replaced by a phenylalanine (F). 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