5-169883110-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001129891.3(INSYN2B):c.789C>A(p.Ser263Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000683 in 1,551,666 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001129891.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INSYN2B | NM_001129891.3 | c.789C>A | p.Ser263Arg | missense_variant | 2/4 | ENST00000377365.4 | |
DOCK2 | NM_004946.3 | c.2799+42258G>T | intron_variant | ENST00000520908.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSYN2B | ENST00000377365.4 | c.789C>A | p.Ser263Arg | missense_variant | 2/4 | 2 | NM_001129891.3 | P1 | |
DOCK2 | ENST00000520908.7 | c.2799+42258G>T | intron_variant | 2 | NM_004946.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 23AN: 155886Hom.: 1 AF XY: 0.000182 AC XY: 15AN XY: 82558
GnomAD4 exome AF: 0.0000657 AC: 92AN: 1399360Hom.: 2 Cov.: 32 AF XY: 0.0000855 AC XY: 59AN XY: 690192
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.789C>A (p.S263R) alteration is located in exon 2 (coding exon 1) of the FAM196B gene. This alteration results from a C to A substitution at nucleotide position 789, causing the serine (S) at amino acid position 263 to be replaced by an arginine (R). 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