chr12-57726635-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_ModerateBS2
The NM_001122772.3(AGAP2):āc.3496A>Gā(p.Ser1166Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000477 in 1,047,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001122772.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGAP2 | NM_001122772.3 | c.3496A>G | p.Ser1166Gly | missense_variant | 19/19 | ENST00000547588.6 | NP_001116244.1 | |
AGAP2-AS1 | NR_027032.1 | n.139+257T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGAP2 | ENST00000547588.6 | c.3496A>G | p.Ser1166Gly | missense_variant | 19/19 | 1 | NM_001122772.3 | ENSP00000449241 | P3 | |
AGAP2-AS1 | ENST00000542466.2 | n.108+257T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000477 AC: 5AN: 1047240Hom.: 0 Cov.: 32 AF XY: 0.00000606 AC XY: 3AN XY: 494748
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 10, 2022 | The c.3496A>G (p.S1166G) alteration is located in exon 19 (coding exon 19) of the AGAP2 gene. This alteration results from a A to G substitution at nucleotide position 3496, causing the serine (S) at amino acid position 1166 to be replaced by a glycine (G). 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