chr8-85463769-A-AGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC

Variant names:

• chr8-85463769-A-AGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC
• ENST00000654303.1:n.32_33insGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCC

Variant summary

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

The ENST00000654303.1(CA3-AS1):​n.32_33insGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCC 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 0.0000233 in 85,810 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: not found (cov: 0)
  • Exomes 𝑓: 0.000023 (0 hom.)
• Consequence: CA3-AS1 ENST00000654303.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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]

ACMG classification

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-AS1	NR_121630.1	n.334+812_334+813insGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2
CA3-AS1	NR_121631.1	n.106+458_106+459insGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2
CA2	NM_000067.3	c.-313_-312insGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC		upstream_gene_variant		ENST00000285379.10	NP_000058.1
CA2	NM_001293675.2	c.-497_-496insGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC		upstream_gene_variant			NP_001280604.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA2	ENST00000285379.10	c.-313_-312insGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC		upstream_gene_variant		1	NM_000067.3	ENSP00000285379.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000233 AC: 2 AN: 85810 Hom.: 0 AF XY: 0.0000425 AC XY: 2 AN XY: 47016

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000384

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-86375998;