rs12767142
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_145868.2(ANXA11):c.1335+94A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,589,450 control chromosomes in the GnomAD database, including 1,237 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.025 ( 55 hom., cov: 32)
Exomes 𝑓: 0.038 ( 1182 hom. )
Consequence
ANXA11
NM_145868.2 intron
NM_145868.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.181
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 10-80157873-T-C is Benign according to our data. Variant chr10-80157873-T-C is described in ClinVar as [Benign]. Clinvar id is 1693168.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0252 (3828/152074) while in subpopulation NFE AF= 0.0391 (2654/67956). AF 95% confidence interval is 0.0378. There are 55 homozygotes in gnomad4. There are 1838 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 3830 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANXA11 | NM_145868.2 | c.1335+94A>G | intron_variant | ENST00000422982.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANXA11 | ENST00000422982.8 | c.1335+94A>G | intron_variant | 1 | NM_145868.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0252 AC: 3830AN: 151956Hom.: 55 Cov.: 32
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GnomAD4 exome AF: 0.0378 AC: 54368AN: 1437376Hom.: 1182 Cov.: 28 AF XY: 0.0380 AC XY: 27135AN XY: 713662
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GnomAD4 genome ? AF: 0.0252 AC: 3828AN: 152074Hom.: 55 Cov.: 32 AF XY: 0.0247 AC XY: 1838AN XY: 74332
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inclusion body myopathy and brain white matter abnormalities Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at