chr10-127175905-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039762.3(INSYN2A):c.491C>T(p.Ala164Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,614,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 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
Genome browser will be placed here
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.491C>T | p.Ala164Val | missense_variant | 4/6 | ENST00000522781.6 | |
DOCK1 | NM_001290223.2 | c.2847+48141G>A | intron_variant | ENST00000623213.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSYN2A | ENST00000522781.6 | c.491C>T | p.Ala164Val | missense_variant | 4/6 | 2 | NM_001039762.3 | P1 | |
DOCK1 | ENST00000623213.2 | c.2847+48141G>A | intron_variant | 1 | NM_001290223.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251460Hom.: 0 AF XY: 0.000235 AC XY: 32AN XY: 135916
GnomAD4 exome AF: 0.000109 AC: 160AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.000113 AC XY: 82AN XY: 727242
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.491C>T (p.A164V) alteration is located in exon 4 (coding exon 1) of the FAM196A gene. This alteration results from a C to T substitution at nucleotide position 491, causing the alanine (A) at amino acid position 164 to be replaced by a valine (V). 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