rs61737563
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_018685.5(ANLN):āc.553A>Cā(p.Arg185=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0896 in 1,613,920 control chromosomes in the GnomAD database, including 7,200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.077 ( 530 hom., cov: 33)
Exomes š: 0.091 ( 6670 hom. )
Consequence
ANLN
NM_018685.5 synonymous
NM_018685.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.06
Genes affected
ANLN (HGNC:14082): (anillin, actin binding protein) This gene encodes an actin-binding protein that plays a role in cell growth and migration, and in cytokinesis. The encoded protein is thought to regulate actin cytoskeletal dynamics in podocytes, components of the glomerulus. Mutations in this gene are associated with focal segmental glomerulosclerosis 8. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 7-36406246-A-C is Benign according to our data. Variant chr7-36406246-A-C is described in ClinVar as [Benign]. Clinvar id is 261050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=3.06 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANLN | NM_018685.5 | c.553A>C | p.Arg185= | synonymous_variant | 4/24 | ENST00000265748.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANLN | ENST00000265748.7 | c.553A>C | p.Arg185= | synonymous_variant | 4/24 | 1 | NM_018685.5 | P2 | |
ANLN | ENST00000396068.6 | c.553A>C | p.Arg185= | synonymous_variant | 4/23 | 1 | A2 | ||
ANLN | ENST00000424865.1 | c.487A>C | p.Arg163= | synonymous_variant | 4/4 | 3 | |||
ANLN | ENST00000460598.1 | n.140A>C | non_coding_transcript_exon_variant | 2/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0773 AC: 11769AN: 152168Hom.: 530 Cov.: 33
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GnomAD3 exomes AF: 0.0722 AC: 18145AN: 251392Hom.: 836 AF XY: 0.0720 AC XY: 9789AN XY: 135876
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GnomAD4 exome AF: 0.0908 AC: 132776AN: 1461634Hom.: 6670 Cov.: 30 AF XY: 0.0895 AC XY: 65084AN XY: 727070
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GnomAD4 genome ? AF: 0.0774 AC: 11781AN: 152286Hom.: 530 Cov.: 33 AF XY: 0.0737 AC XY: 5485AN XY: 74470
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 29, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 18, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Focal segmental glomerulosclerosis 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at