10-80156034-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145868.2(ANXA11):c.1459-122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 1,006,106 control chromosomes in the GnomAD database, including 450,783 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.94 ( 66661 hom., cov: 33)
Exomes 𝑓: 0.95 ( 384122 hom. )
Consequence
ANXA11
NM_145868.2 intron
NM_145868.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.141
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 10-80156034-T-C is Benign according to our data. Variant chr10-80156034-T-C is described in ClinVar as [Benign]. Clinvar id is 1248519.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA11 | NM_145868.2 | c.1459-122A>G | intron_variant | ENST00000422982.8 | NP_665875.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA11 | ENST00000422982.8 | c.1459-122A>G | intron_variant | 1 | NM_145868.2 | ENSP00000404412 | P2 |
Frequencies
GnomAD3 genomes AF: 0.936 AC: 142367AN: 152176Hom.: 66603 Cov.: 33
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GnomAD4 exome AF: 0.948 AC: 809683AN: 853812Hom.: 384122 AF XY: 0.949 AC XY: 417929AN XY: 440556
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GnomAD4 genome AF: 0.936 AC: 142481AN: 152294Hom.: 66661 Cov.: 33 AF XY: 0.936 AC XY: 69716AN XY: 74466
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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