2-235494710-C-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001037131.3(AGAP1):c.24C>A(p.Ala8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000129 in 1,549,958 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 29)
Exomes 𝑓: 7.1e-7 ( 0 hom. )
Consequence
AGAP1
NM_001037131.3 synonymous
NM_001037131.3 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 2.49
Genes affected
AGAP1 (HGNC:16922): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 1) This gene encodes a member of an ADP-ribosylation factor GTPase-activating protein family involved in membrane trafficking and cytoskeleton dynamics. This gene functions as a direct regulator of the adaptor-related protein complex 3 on endosomes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
Variant 2-235494710-C-A is Benign according to our data. Variant chr2-235494710-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2132348.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.49 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGAP1 | NM_001037131.3 | c.24C>A | p.Ala8= | synonymous_variant | 1/18 | ENST00000304032.13 | |
AGAP1 | NM_014914.5 | c.24C>A | p.Ala8= | synonymous_variant | 1/17 | ||
AGAP1 | NM_001244888.2 | c.24C>A | p.Ala8= | synonymous_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGAP1 | ENST00000304032.13 | c.24C>A | p.Ala8= | synonymous_variant | 1/18 | 5 | NM_001037131.3 |
Frequencies
GnomAD3 genomes AF: 0.00000667 AC: 1AN: 149924Hom.: 0 Cov.: 29
GnomAD3 genomes
AF:
AC:
1
AN:
149924
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 7.14e-7 AC: 1AN: 1400034Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 696410
GnomAD4 exome
AF:
AC:
1
AN:
1400034
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
696410
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000667 AC: 1AN: 149924Hom.: 0 Cov.: 29 AF XY: 0.0000137 AC XY: 1AN XY: 73164
GnomAD4 genome
AF:
AC:
1
AN:
149924
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
73164
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 30, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at