rs3809828
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_014716.4(ACAP1):c.498C>T(p.Tyr166=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 1,613,662 control chromosomes in the GnomAD database, including 3,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.050 ( 292 hom., cov: 31)
Exomes 𝑓: 0.057 ( 2748 hom. )
Consequence
ACAP1
NM_014716.4 synonymous
NM_014716.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.86
Genes affected
ACAP1 (HGNC:16467): (ArfGAP with coiled-coil, ankyrin repeat and PH domains 1) Predicted to enable GTPase activator activity and metal ion binding activity. Predicted to be involved in protein transport and regulation of catalytic activity. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP7
Synonymous conserved (PhyloP=1.86 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAP1 | NM_014716.4 | c.498C>T | p.Tyr166= | synonymous_variant | 6/22 | ENST00000158762.8 | |
ACAP1 | XM_047437150.1 | c.276C>T | p.Tyr92= | synonymous_variant | 6/22 | ||
ACAP1 | XM_047437151.1 | c.276C>T | p.Tyr92= | synonymous_variant | 5/21 | ||
ACAP1 | XM_047437152.1 | c.498C>T | p.Tyr166= | synonymous_variant | 6/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAP1 | ENST00000158762.8 | c.498C>T | p.Tyr166= | synonymous_variant | 6/22 | 1 | NM_014716.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0504 AC: 7664AN: 152078Hom.: 292 Cov.: 31
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GnomAD3 exomes AF: 0.0644 AC: 16136AN: 250410Hom.: 710 AF XY: 0.0635 AC XY: 8603AN XY: 135444
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GnomAD4 exome AF: 0.0571 AC: 83519AN: 1461466Hom.: 2748 Cov.: 31 AF XY: 0.0567 AC XY: 41239AN XY: 727010
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GnomAD4 genome AF: 0.0504 AC: 7671AN: 152196Hom.: 292 Cov.: 31 AF XY: 0.0519 AC XY: 3860AN XY: 74414
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ClinVar
Not reported inComputational scores
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Name
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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