rs17213431
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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):c.1857G>A(p.Val619=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,612,792 control chromosomes in the GnomAD database, including 14,460 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.097 ( 923 hom., cov: 32)
Exomes 𝑓: 0.13 ( 13537 hom. )
Consequence
ANLN
NM_018685.5 synonymous
NM_018685.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.02
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=-0.58).
BP6
?
Variant 7-36419467-G-A is Benign according to our data. Variant chr7-36419467-G-A is described in ClinVar as [Benign]. Clinvar id is 1165187.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.02 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANLN | NM_018685.5 | c.1857G>A | p.Val619= | synonymous_variant | 10/24 | ENST00000265748.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANLN | ENST00000265748.7 | c.1857G>A | p.Val619= | synonymous_variant | 10/24 | 1 | NM_018685.5 | P2 | |
ANLN | ENST00000396068.6 | c.1746G>A | p.Val582= | synonymous_variant | 9/23 | 1 | A2 | ||
ANLN | ENST00000428612.5 | c.97-5078G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0972 AC: 14782AN: 152072Hom.: 927 Cov.: 32
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GnomAD3 exomes AF: 0.112 AC: 27937AN: 250110Hom.: 1851 AF XY: 0.118 AC XY: 16001AN XY: 135214
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GnomAD4 exome AF: 0.132 AC: 192204AN: 1460602Hom.: 13537 Cov.: 32 AF XY: 0.133 AC XY: 96336AN XY: 726654
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GnomAD4 genome ? AF: 0.0971 AC: 14776AN: 152190Hom.: 923 Cov.: 32 AF XY: 0.0978 AC XY: 7275AN XY: 74388
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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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