rs57677078

Variant summary

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

The NM_004056.6(CA8):​c.*36-13_*36-9delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000183 in 109,306 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 0.000018 ( 0 hom., cov: 26)
Failed GnomAD Quality Control

Consequence

CA8
NM_004056.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.495
Variant links:
Genes affected
CA8 (HGNC:1382): (carbonic anhydrase 8) The protein encoded by this gene was initially named CA-related protein because of sequence similarity to other known carbonic anhydrase genes. However, the gene product lacks carbonic anhydrase activity (i.e., the reversible hydration of carbon dioxide). The gene product continues to carry a carbonic anhydrase designation based on clear sequence identity to other members of the carbonic anhydrase gene family. The absence of CA8 gene transcription in the cerebellum of the lurcher mutant in mice with a neurologic defect suggests an important role for this acatalytic form. Mutations in this gene are associated with cerebellar ataxia, mental retardation, and dysequilibrium syndrome 3 (CMARQ3). Polymorphisms in this gene are associated with osteoporosis, and overexpression of this gene in osteosarcoma cells suggests an oncogenic role. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

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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
CA8NM_004056.6 linkc.*36-13_*36-9delTTTTT intron_variant Intron 8 of 8 ENST00000317995.5 NP_004047.3 P35219
CA8NM_001321839.2 linkc.*36-13_*36-9delTTTTT intron_variant Intron 7 of 7 NP_001308768.1 P35219
CA8NR_135821.2 linkn.1212-13_1212-9delTTTTT intron_variant Intron 9 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CA8ENST00000317995.5 linkc.*36-13_*36-9delTTTTT intron_variant Intron 8 of 8 1 NM_004056.6 ENSP00000314407.4 P35219

Frequencies

GnomAD3 genomes
AF:
0.0000183
AC:
2
AN:
109306
Hom.:
0
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.0000288
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000103
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000183
AC:
2
AN:
109306
Hom.:
0
Cov.:
26
AF XY:
0.0000191
AC XY:
1
AN XY:
52246
show subpopulations
Gnomad4 AFR
AF:
0.0000288
Gnomad4 AMR
AF:
0.000103
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
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: rs57677078; hg19: chr8-61102552; API