chr10-80157650-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_145868.2(ANXA11):c.1449C>T(p.His483=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,452 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
ANXA11
NM_145868.2 synonymous
NM_145868.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.93
Genes affected
ANXA11 (HGNC:535): (annexin A11) This gene encodes a member of the annexin family, a group of calcium-dependent phospholipid-binding proteins. Annexins have unique N-terminal domains and conserved C-terminal domains, which contain calcium-dependent phospholipid-binding sites. The encoded protein is a 56-kD antigen recognized by sera from patients with various autoimmune diseases. Several transcript variants encoding two different isoforms have been identified. [provided by RefSeq, Dec 2015]
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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=-0.7).
BP6
Variant 10-80157650-G-A is Benign according to our data. Variant chr10-80157650-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1931024.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA11 | NM_145868.2 | c.1449C>T | p.His483= | synonymous_variant | 15/16 | ENST00000422982.8 | NP_665875.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA11 | ENST00000422982.8 | c.1449C>T | p.His483= | synonymous_variant | 15/16 | 1 | NM_145868.2 | ENSP00000404412 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152042Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250874Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135572
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GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461410Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726958
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GnomAD4 genome AF: 0.0000592 AC: 9AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74256
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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 | Mar 24, 2023 | - - |
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