chr8-85463901-A-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NR_121630.1(CA3-AS1):n.334+681T>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 0.984 in 550,414 control chromosomes in the GnomAD database, including 266,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.99 ( 72383 hom., cov: 22)
Exomes 𝑓: 0.98 ( 194264 hom. )
Consequence
CA3-AS1
NR_121630.1 intron, non_coding_transcript
NR_121630.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.147
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=-0.62).
BP6
Variant 8-85463901-A-T is Benign according to our data. Variant chr8-85463901-A-T is described in ClinVar as [Benign]. Clinvar id is 369615.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA3-AS1 | NR_121630.1 | n.334+681T>A | intron_variant, non_coding_transcript_variant | |||||
CA3-AS1 | NR_121631.1 | n.106+327T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CA3-AS1 | ENST00000521761.6 | n.334+681T>A | intron_variant, non_coding_transcript_variant | 4 | ||||||
CA3-AS1 | ENST00000517697.6 | n.193+327T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.986 AC: 146745AN: 148860Hom.: 72331 Cov.: 22
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GnomAD4 exome AF: 0.984 AC: 394950AN: 401450Hom.: 194264 Cov.: 5 AF XY: 0.984 AC XY: 218597AN XY: 222086
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GnomAD4 genome AF: 0.986 AC: 146849AN: 148964Hom.: 72383 Cov.: 22 AF XY: 0.986 AC XY: 71743AN XY: 72766
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Osteopetrosis with renal tubular acidosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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