chr10-80157637-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_145868.2(ANXA11):c.1458+4C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000945 in 1,612,450 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0050 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00052 ( 3 hom. )
Consequence
ANXA11
NM_145868.2 splice_donor_region, intron
NM_145868.2 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00006004
2
Clinical Significance
Conservation
PhyloP100: -0.954
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=-0.88).
BP6
Variant 10-80157637-G-A is Benign according to our data. Variant chr10-80157637-G-A is described in ClinVar as [Benign]. Clinvar id is 1643018.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00501 (763/152174) while in subpopulation AFR AF= 0.017 (706/41534). AF 95% confidence interval is 0.016. There are 4 homozygotes in gnomad4. There are 338 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 763 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA11 | NM_145868.2 | c.1458+4C>T | splice_donor_region_variant, intron_variant | ENST00000422982.8 | NP_665875.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA11 | ENST00000422982.8 | c.1458+4C>T | splice_donor_region_variant, intron_variant | 1 | NM_145868.2 | ENSP00000404412 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00498 AC: 757AN: 152056Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00127 AC: 317AN: 249934Hom.: 1 AF XY: 0.000970 AC XY: 131AN XY: 135100
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GnomAD4 exome AF: 0.000521 AC: 761AN: 1460276Hom.: 3 Cov.: 32 AF XY: 0.000441 AC XY: 320AN XY: 726296
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GnomAD4 genome AF: 0.00501 AC: 763AN: 152174Hom.: 4 Cov.: 32 AF XY: 0.00454 AC XY: 338AN XY: 74396
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 04, 2023 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at