3-195392120-A-G
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_012287.6(ACAP2):āc.81T>Cā(p.Asp27Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,612,996 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00022 ( 1 hom., cov: 31)
Exomes š: 0.000053 ( 1 hom. )
Consequence
ACAP2
NM_012287.6 synonymous
NM_012287.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.52
Genes affected
ACAP2 (HGNC:16469): (ArfGAP with coiled-coil, ankyrin repeat and PH domains 2) Enables GTPase activator activity. Acts upstream of or within actin filament-based process. Located in ruffle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant 3-195392120-A-G is Benign according to our data. Variant chr3-195392120-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 785079.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.52 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACAP2 | NM_012287.6 | c.81T>C | p.Asp27Asp | synonymous_variant | 2/23 | ENST00000326793.11 | NP_036419.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACAP2 | ENST00000326793.11 | c.81T>C | p.Asp27Asp | synonymous_variant | 2/23 | 1 | NM_012287.6 | ENSP00000324287.6 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152228Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250488Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135444
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GnomAD4 exome AF: 0.0000527 AC: 77AN: 1460650Hom.: 1 Cov.: 29 AF XY: 0.0000385 AC XY: 28AN XY: 726578
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GnomAD4 genome AF: 0.000217 AC: 33AN: 152346Hom.: 1 Cov.: 31 AF XY: 0.000242 AC XY: 18AN XY: 74516
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jun 13, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at