chr8-85463769-A-AGGAGCCCC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000654303.1(CA3-AS1):n.25_32dupGGGGCTCC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 231,744 control chromosomes in the GnomAD database, including 33,341 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.57 ( 24746 hom., cov: 0)
Exomes 𝑓: 0.38 ( 8595 hom. )
Consequence
CA3-AS1
ENST00000654303.1 non_coding_transcript_exon
ENST00000654303.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00800
Genes affected
CA2 (HGNC:1373): (carbonic anhydrase 2) The protein encoded by this gene is one of several isozymes of carbonic anhydrase, which catalyzes reversible hydration of carbon dioxide. Defects in this enzyme are associated with osteopetrosis and renal tubular acidosis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 8-85463769-A-AGGAGCCCC is Benign according to our data. Variant chr8-85463769-A-AGGAGCCCC is described in ClinVar as [Benign]. Clinvar id is 1225462.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA3-AS1 | NR_121630.1 | n.334+805_334+812dupGGGGCTCC | intron_variant | Intron 1 of 2 | ||||
CA3-AS1 | NR_121631.1 | n.106+451_106+458dupGGGGCTCC | intron_variant | Intron 1 of 2 | ||||
CA2 | NM_000067.3 | c.-313_-312insGGAGCCCC | upstream_gene_variant | ENST00000285379.10 | NP_000058.1 | |||
CA2 | NM_001293675.2 | c.-497_-496insGGAGCCCC | upstream_gene_variant | NP_001280604.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.574 AC: 84047AN: 146442Hom.: 24730 Cov.: 0
GnomAD3 genomes
AF:
AC:
84047
AN:
146442
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.380 AC: 32354AN: 85216Hom.: 8595 AF XY: 0.367 AC XY: 17148AN XY: 46706
GnomAD4 exome
AF:
AC:
32354
AN:
85216
Hom.:
AF XY:
AC XY:
17148
AN XY:
46706
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.574 AC: 84090AN: 146528Hom.: 24746 Cov.: 0 AF XY: 0.576 AC XY: 41147AN XY: 71450
GnomAD4 genome
AF:
AC:
84090
AN:
146528
Hom.:
Cov.:
0
AF XY:
AC XY:
41147
AN XY:
71450
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 11, 2020
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at