chr10-122456893-T-TG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001099667.3(ARMS2):c.298-14_298-13insG variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00289 in 1,542,698 control chromosomes in the GnomAD database, including 60 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 29 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 31 hom. )
Consequence
ARMS2
NM_001099667.3 splice_polypyrimidine_tract, intron
NM_001099667.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.213
Genes affected
ARMS2 (HGNC:32685): (age-related maculopathy susceptibility 2) This gene encodes a small secreted protein specific to primates. This protein is a component of the choroidal extracellular matrix of the eye. Mutations in this gene are associated with age-related macular degeneration. [provided by RefSeq, Sep 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 10-122456893-T-TG is Benign according to our data. Variant chr10-122456893-T-TG is described in ClinVar as [Likely_benign]. Clinvar id is 299030.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0118 (1802/152134) while in subpopulation AFR AF= 0.0397 (1645/41460). AF 95% confidence interval is 0.0381. There are 29 homozygotes in gnomad4. There are 849 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMS2 | NM_001099667.3 | c.298-14_298-13insG | splice_polypyrimidine_tract_variant, intron_variant | ENST00000528446.1 | |||
LOC105378525 | XR_946382.3 | n.1874+1601_1874+1602insC | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMS2 | ENST00000528446.1 | c.298-14_298-13insG | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001099667.3 | P1 | |||
ENST00000650300.1 | n.1852+1601_1852+1602insC | intron_variant, non_coding_transcript_variant | |||||||
ENST00000647969.1 | n.182+1601_182+1602insC | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0118 AC: 1796AN: 152016Hom.: 29 Cov.: 32
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GnomAD3 exomes AF: 0.00347 AC: 521AN: 150120Hom.: 10 AF XY: 0.00358 AC XY: 285AN XY: 79512
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GnomAD4 exome AF: 0.00191 AC: 2657AN: 1390564Hom.: 31 Cov.: 33 AF XY: 0.00201 AC XY: 1379AN XY: 685728
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GnomAD4 genome ? AF: 0.0118 AC: 1802AN: 152134Hom.: 29 Cov.: 32 AF XY: 0.0114 AC XY: 849AN XY: 74368
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Macular degeneration Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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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