chr10-122456894-AT-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001099667.3(ARMS2):c.298-4del 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 0.000743 in 1,510,532 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 2 hom. )
Consequence
ARMS2
NM_001099667.3 splice_polypyrimidine_tract, intron
NM_001099667.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0310
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 Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 10-122456894-AT-A is Benign according to our data. Variant chr10-122456894-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 299033.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMS2 | NM_001099667.3 | c.298-4del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000528446.1 | |||
LOC105378525 | XR_946382.3 | n.1874+1600del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMS2 | ENST00000528446.1 | c.298-4del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001099667.3 | P1 | |||
ENST00000650300.1 | n.1852+1600del | intron_variant, non_coding_transcript_variant | |||||||
ENST00000647969.1 | n.182+1600del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00375 AC: 566AN: 151082Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00111 AC: 155AN: 139318Hom.: 0 AF XY: 0.000745 AC XY: 55AN XY: 73790
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GnomAD4 exome AF: 0.000410 AC: 558AN: 1359330Hom.: 2 Cov.: 32 AF XY: 0.000367 AC XY: 246AN XY: 670518
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GnomAD4 genome ? AF: 0.00374 AC: 565AN: 151202Hom.: 1 Cov.: 32 AF XY: 0.00365 AC XY: 269AN XY: 73798
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at