10-50008774-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001077665.3(AGAP6):c.649T>C(p.Ser217Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGAP6 | ENST00000412531.7 | c.649T>C | p.Ser217Pro | missense_variant | Exon 8 of 8 | 1 | NM_001077665.3 | ENSP00000500374.1 | ||
TIMM23B-AGAP6 | ENST00000651763.1 | n.*864T>C | non_coding_transcript_exon_variant | Exon 17 of 18 | ENSP00000502214.1 | |||||
TIMM23B-AGAP6 | ENST00000651763.1 | n.*864T>C | 3_prime_UTR_variant | Exon 17 of 18 | ENSP00000502214.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152108Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000371 AC: 3AN: 80812Hom.: 0 AF XY: 0.0000254 AC XY: 1AN XY: 39434
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461866Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727232
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152108Hom.: 0 Cov.: 30 AF XY: 0.0000538 AC XY: 4AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.649T>C (p.S217P) alteration is located in exon 8 (coding exon 8) of the AGAP6 gene. This alteration results from a T to C substitution at nucleotide position 649, causing the serine (S) at amino acid position 217 to be replaced by a proline (P). 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