5-52989268-G-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000662246.1(ITGA2-AS1):n.75+822C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0672 in 650,998 control chromosomes in the GnomAD database, including 1,921 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.059 ( 375 hom., cov: 32)
Exomes 𝑓: 0.070 ( 1546 hom. )
Consequence
ITGA2-AS1
ENST00000662246.1 intron, non_coding_transcript
ENST00000662246.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.27
Genes affected
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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=-0.89).
BP6
Variant 5-52989268-G-T is Benign according to our data. Variant chr5-52989268-G-T is described in ClinVar as [Benign]. Clinvar id is 1249583.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0768 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA2-AS1 | ENST00000662246.1 | n.75+822C>A | intron_variant, non_coding_transcript_variant | |||||||
ITGA2-AS1 | ENST00000503559.1 | n.189+822C>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
ITGA2-AS1 | ENST00000505701.5 | n.189+822C>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0595 AC: 9019AN: 151620Hom.: 374 Cov.: 32
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GnomAD4 exome AF: 0.0696 AC: 34744AN: 499266Hom.: 1546 AF XY: 0.0679 AC XY: 17905AN XY: 263836
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GnomAD4 genome AF: 0.0594 AC: 9017AN: 151732Hom.: 375 Cov.: 32 AF XY: 0.0608 AC XY: 4513AN XY: 74188
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at