chr12-57741915-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000257897.7(AGAP2):c.157C>A(p.Arg53=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00301 in 1,613,162 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0031 ( 18 hom. )
Consequence
AGAP2
ENST00000257897.7 synonymous
ENST00000257897.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.12
Genes affected
AGAP2 (HGNC:16921): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 2) The protein encoded by this gene belongs to the centaurin gamma-like family. It mediates anti-apoptotic effects of nerve growth factor by activating nuclear phosphoinositide 3-kinase. It is overexpressed in cancer cells, and promotes cancer cell invasion. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
TSPAN31 (HGNC:10539): (tetraspanin 31) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is thought to be involved in growth-related cellular processes. This gene is associated with tumorigenesis and osteosarcoma. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 12-57741915-G-T is Benign according to our data. Variant chr12-57741915-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643150.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 274 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGAP2 | NM_014770.4 | c.157C>A | p.Arg53= | synonymous_variant | 1/18 | NP_055585.1 | ||
AGAP2 | XM_005268626.3 | c.157C>A | p.Arg53= | synonymous_variant | 1/19 | XP_005268683.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGAP2 | ENST00000257897.7 | c.157C>A | p.Arg53= | synonymous_variant | 1/18 | 1 | ENSP00000257897 | A1 | ||
TSPAN31 | ENST00000547311.5 | n.235+1945G>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
TSPAN31 | ENST00000550528.5 | n.105+1945G>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
TSPAN31 | ENST00000553221.5 | n.190-1325G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00180 AC: 274AN: 152158Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00140 AC: 351AN: 250968Hom.: 0 AF XY: 0.00129 AC XY: 175AN XY: 135644
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GnomAD4 exome AF: 0.00313 AC: 4579AN: 1461004Hom.: 18 Cov.: 33 AF XY: 0.00292 AC XY: 2121AN XY: 726676
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GnomAD4 genome AF: 0.00180 AC: 274AN: 152158Hom.: 1 Cov.: 32 AF XY: 0.00144 AC XY: 107AN XY: 74322
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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 | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | AGAP2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at