10-49988842-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001077665.3(AGAP6):c.127G>T(p.Ala43Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000207 in 1,446,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001077665.3 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 |
---|---|---|---|---|---|---|---|
AGAP6 | NM_001077665.3 | c.127G>T | p.Ala43Ser | missense_variant | 1/8 | ENST00000412531.7 | |
TIMM23B-AGAP6 | NR_158661.1 | n.1353G>T | non_coding_transcript_exon_variant | 10/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGAP6 | ENST00000412531.7 | c.127G>T | p.Ala43Ser | missense_variant | 1/8 | 1 | NM_001077665.3 | A2 | |
ENST00000650407.1 | n.58C>A | non_coding_transcript_exon_variant | 1/4 |
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD3 exomes AF: 0.00000421 AC: 1AN: 237584Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129576
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1446616Hom.: 0 Cov.: 78 AF XY: 0.00000278 AC XY: 2AN XY: 719992
GnomAD4 genome Cov.: 29
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at