12-57742067-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014770.4(AGAP2):āc.5A>Gā(p.His2Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014770.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGAP2 | NM_014770.4 | c.5A>G | p.His2Arg | missense_variant | 1/18 | NP_055585.1 | ||
AGAP2 | XM_005268626.3 | c.5A>G | p.His2Arg | missense_variant | 1/19 | XP_005268683.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGAP2 | ENST00000257897.7 | c.5A>G | p.His2Arg | missense_variant | 1/18 | 1 | ENSP00000257897.3 | |||
TSPAN31 | ENST00000547311.5 | n.235+2097T>C | intron_variant | 3 | ||||||
TSPAN31 | ENST00000550528.5 | n.105+2097T>C | intron_variant | 3 | ||||||
TSPAN31 | ENST00000553221.5 | n.190-1173T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251230Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135780
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461716Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 727166
GnomAD4 genome AF: 0.000131 AC: 20AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2023 | The c.5A>G (p.H2R) alteration is located in exon 1 (coding exon 1) of the AGAP2 gene. This alteration results from a A to G substitution at nucleotide position 5, causing the histidine (H) at amino acid position 2 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