chr10-127175735-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001039762.3(INSYN2A):c.661G>T(p.Asp221Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,822 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D221N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001039762.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INSYN2A | NM_001039762.3 | c.661G>T | p.Asp221Tyr | missense_variant | 4/6 | ENST00000522781.6 | |
DOCK1 | NM_001290223.2 | c.2847+47971C>A | intron_variant | ENST00000623213.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSYN2A | ENST00000522781.6 | c.661G>T | p.Asp221Tyr | missense_variant | 4/6 | 2 | NM_001039762.3 | P1 | |
DOCK1 | ENST00000623213.2 | c.2847+47971C>A | intron_variant | 1 | NM_001290223.2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727214
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2022 | The c.661G>T (p.D221Y) alteration is located in exon 4 (coding exon 1) of the FAM196A gene. This alteration results from a G to T substitution at nucleotide position 661, causing the aspartic acid (D) at amino acid position 221 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.