10-49988935-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001077665.3(AGAP6):āc.220G>Cā(p.Glu74Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000418 in 1,601,544 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001077665.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGAP6 | NM_001077665.3 | c.220G>C | p.Glu74Gln | missense_variant | 1/8 | ENST00000412531.7 | NP_001071133.2 | |
TIMM23B-AGAP6 | NR_158661.1 | n.1446G>C | non_coding_transcript_exon_variant | 10/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGAP6 | ENST00000412531.7 | c.220G>C | p.Glu74Gln | missense_variant | 1/8 | 1 | NM_001077665.3 | ENSP00000500374 | A2 | |
ENST00000650407.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151656Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000789 AC: 19AN: 240824Hom.: 1 AF XY: 0.0000839 AC XY: 11AN XY: 131066
GnomAD4 exome AF: 0.0000428 AC: 62AN: 1449770Hom.: 2 Cov.: 61 AF XY: 0.0000513 AC XY: 37AN XY: 721562
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151774Hom.: 0 Cov.: 29 AF XY: 0.0000270 AC XY: 2AN XY: 74150
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.220G>C (p.E74Q) alteration is located in exon 1 (coding exon 1) of the AGAP6 gene. This alteration results from a G to C substitution at nucleotide position 220, causing the glutamic acid (E) at amino acid position 74 to be replaced by a glutamine (Q). 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