5-151122177-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001155.5(ANXA6):c.1317C>T(p.Tyr439=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,598,600 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 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 0 hom. )
Consequence
ANXA6
NM_001155.5 synonymous
NM_001155.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.688
Genes affected
ANXA6 (HGNC:544): (annexin A6) Annexin VI belongs to a family of calcium-dependent membrane and phospholipid binding proteins. Several members of the annexin family have been implicated in membrane-related events along exocytotic and endocytotic pathways. The annexin VI gene is approximately 60 kbp long and contains 26 exons. It encodes a protein of about 68 kDa that consists of eight 68-amino acid repeats separated by linking sequences of variable lengths. It is highly similar to human annexins I and II sequences, each of which contain four such repeats. Annexin VI has been implicated in mediating the endosome aggregation and vesicle fusion in secreting epithelia during exocytosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 5-151122177-G-A is Benign according to our data. Variant chr5-151122177-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2655942.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.688 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANXA6 | NM_001155.5 | c.1317C>T | p.Tyr439= | synonymous_variant | 17/26 | ENST00000354546.10 | |
ANXA6 | NM_001363114.2 | c.1317C>T | p.Tyr439= | synonymous_variant | 17/25 | ||
ANXA6 | NM_001193544.2 | c.1221C>T | p.Tyr407= | synonymous_variant | 16/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANXA6 | ENST00000354546.10 | c.1317C>T | p.Tyr439= | synonymous_variant | 17/26 | 1 | NM_001155.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152086Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000980 AC: 23AN: 234780Hom.: 0 AF XY: 0.0000626 AC XY: 8AN XY: 127850
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GnomAD4 exome AF: 0.000164 AC: 237AN: 1446514Hom.: 0 Cov.: 30 AF XY: 0.000149 AC XY: 107AN XY: 719292
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GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74282
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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 | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | ANXA6: BP4, BP7 - |
Computational scores
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Name
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Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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