chr10-73674675-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144000.4(AGAP5):c.1985C>A(p.Thr662Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,611,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144000.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGAP5 | NM_001144000.4 | c.1985C>A | p.Thr662Asn | missense_variant | 8/8 | ENST00000374094.9 | |
BMS1P4-AGAP5 | NR_160426.1 | n.4252C>A | non_coding_transcript_exon_variant | 20/20 | |||
BMS1P4-AGAP5 | NR_160425.1 | n.3464C>A | non_coding_transcript_exon_variant | 19/19 | |||
BMS1P4-AGAP5 | NR_160427.1 | n.3396C>A | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGAP5 | ENST00000374094.9 | c.1985C>A | p.Thr662Asn | missense_variant | 8/8 | 1 | NM_001144000.4 | A2 | |
SYNPO2L-AS1 | ENST00000668336.1 | n.430G>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152180Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000134 AC: 26AN: 194546Hom.: 0 AF XY: 0.000122 AC XY: 13AN XY: 106356
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1459664Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 726146
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152298Hom.: 0 Cov.: 29 AF XY: 0.0000269 AC XY: 2AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.1985C>A (p.T662N) alteration is located in exon 8 (coding exon 8) of the AGAP5 gene. This alteration results from a C to A substitution at nucleotide position 1985, causing the threonine (T) at amino acid position 662 to be replaced by an asparagine (N). 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