8-85464097-G-A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_000067.3(CA2):​c.16G>A​(p.Gly6Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000517 in 1,547,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000050 ( 0 hom. )

Consequence

CA2
NM_000067.3 missense

Scores

8
10
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.49
Variant links:
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]
CA3-AS1 (HGNC:51657): (CA3 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.946

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CA2NM_000067.3 linkc.16G>A p.Gly6Arg missense_variant Exon 1 of 7 ENST00000285379.10 NP_000058.1 P00918V9HW21
CA2NM_001293675.2 linkc.-169G>A 5_prime_UTR_variant Exon 1 of 6 NP_001280604.1 V9HW21
CA3-AS1NR_121630.1 linkn.334+485C>T intron_variant Intron 1 of 2
CA3-AS1NR_121631.1 linkn.106+131C>T intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CA2ENST00000285379.10 linkc.16G>A p.Gly6Arg missense_variant Exon 1 of 7 1 NM_000067.3 ENSP00000285379.4 P00918

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152160
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
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
GnomAD3 exomes
AF:
0.0000280
AC:
4
AN:
142928
Hom.:
0
AF XY:
0.0000128
AC XY:
1
AN XY:
78014
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000819
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000180
Gnomad OTH exome
AF:
0.000246
GnomAD4 exome
AF:
0.00000501
AC:
7
AN:
1395830
Hom.:
0
Cov.:
32
AF XY:
0.00000290
AC XY:
2
AN XY:
689626
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000550
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:
0.00000370
Gnomad4 OTH exome
AF:
0.0000172
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152160
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
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
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.95
BayesDel_addAF
Uncertain
0.025
T
BayesDel_noAF
Uncertain
-0.010
CADD
Pathogenic
34
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.75
D
Eigen
Pathogenic
0.77
Eigen_PC
Pathogenic
0.67
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.96
D
M_CAP
Pathogenic
0.88
D
MetaRNN
Pathogenic
0.95
D
MetaSVM
Uncertain
0.79
D
MutationAssessor
Pathogenic
3.4
M
PrimateAI
Uncertain
0.65
T
PROVEAN
Pathogenic
-6.0
D
REVEL
Pathogenic
0.80
Sift
Uncertain
0.010
D
Sift4G
Uncertain
0.022
D
Polyphen
1.0
D
Vest4
0.65
MutPred
0.77
Gain of MoRF binding (P = 1e-04);
MVP
0.95
MPC
1.0
ClinPred
0.95
D
GERP RS
4.5
Varity_R
0.96
gMVP
0.91

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.60
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.60
Position offset: 1

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: rs1219072767; hg19: chr8-86376326; API