chr10-80155930-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.1459-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,530 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 0.000092 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
ANXA11
NM_145868.2 intron
NM_145868.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.454
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=-0.78).
BP6
Variant 10-80155930-G-A is Benign according to our data. Variant chr10-80155930-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2984910.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANXA11 | NM_145868.2 | c.1459-18C>T | intron_variant | ENST00000422982.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANXA11 | ENST00000422982.8 | c.1459-18C>T | intron_variant | 1 | NM_145868.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152208Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250060Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135274
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GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460322Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726642
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GnomAD4 genome AF: 0.0000920 AC: 14AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74352
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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 | Invitae | Jun 26, 2023 | - - |
Computational scores
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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