8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000654303.1(CA3-AS1):​n.17_32delGGGGCTCCGGGGCTCC 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 0.0000559 in 232,482 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000055 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000058 ( 0 hom. )

Consequence

CA3-AS1
ENST00000654303.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.28
Variant links:
Genes affected
CA3-AS1 (HGNC:51657): (CA3 antisense RNA 1)
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CA3-AS1NR_121630.1 linkn.334+797_334+812delGGGGCTCCGGGGCTCC intron_variant Intron 1 of 2
CA3-AS1NR_121631.1 linkn.106+443_106+458delGGGGCTCCGGGGCTCC intron_variant Intron 1 of 2
CA2NM_000067.3 linkc.-312_-297delGGAGCCCCGGAGCCCC upstream_gene_variant ENST00000285379.10 NP_000058.1 P00918V9HW21
CA2NM_001293675.2 linkc.-496_-481delGGAGCCCCGGAGCCCC upstream_gene_variant NP_001280604.1 V9HW21

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CA2ENST00000285379.10 linkc.-312_-297delGGAGCCCCGGAGCCCC upstream_gene_variant 1 NM_000067.3 ENSP00000285379.4 P00918

Frequencies

GnomAD3 genomes
AF:
0.0000546
AC:
8
AN:
146586
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000252
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000623
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000606
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000583
AC:
5
AN:
85810
Hom.:
0
AF XY:
0.0000213
AC XY:
1
AN XY:
47016
show subpopulations
Gnomad4 AFR exome
AF:
0.00104
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000654
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000577
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000545
AC:
8
AN:
146672
Hom.:
0
Cov.:
0
AF XY:
0.0000559
AC XY:
4
AN XY:
71516
show subpopulations
Gnomad4 AFR
AF:
0.0000252
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000625
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000606
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs77895131; hg19: chr8-86375998; API