8-85383194-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000520921.1(CA3):​c.-239C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.071 in 152,310 control chromosomes in the GnomAD database, including 564 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.071 ( 563 hom., cov: 32)
Exomes 𝑓: 0.077 ( 1 hom. )

Consequence

CA3
ENST00000520921.1 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.389
Variant links:
Genes affected
CA3 (HGNC:1374): (carbonic anhydrase 3) Carbonic anhydrase III (CAIII) is a member of a multigene family (at least six separate genes are known) that encodes carbonic anhydrase isozymes. These carbonic anhydrases are a class of metalloenzymes that catalyze the reversible hydration of carbon dioxide and are differentially expressed in a number of cell types. The expression of the CA3 gene is strictly tissue specific and present at high levels in skeletal muscle and much lower levels in cardiac and smooth muscle. A proportion of carriers of Duchenne muscle dystrophy have a higher CA3 level than normal. The gene spans 10.3 kb and contains seven exons and six introns. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CA3ENST00000520921.1 linkc.-239C>T 5_prime_UTR_variant 2/44 ENSP00000429760.1 E5RHI4

Frequencies

GnomAD3 genomes
AF:
0.0710
AC:
10802
AN:
152088
Hom.:
563
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0211
Gnomad AMI
AF:
0.0647
Gnomad AMR
AF:
0.0523
Gnomad ASJ
AF:
0.0708
Gnomad EAS
AF:
0.00173
Gnomad SAS
AF:
0.0319
Gnomad FIN
AF:
0.166
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.0988
Gnomad OTH
AF:
0.0738
GnomAD4 exome
AF:
0.0769
AC:
8
AN:
104
Hom.:
1
Cov.:
0
AF XY:
0.0735
AC XY:
5
AN XY:
68
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 FIN exome
AF:
0.0385
Gnomad4 NFE exome
AF:
0.0938
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0710
AC:
10803
AN:
152206
Hom.:
563
Cov.:
32
AF XY:
0.0728
AC XY:
5420
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0211
Gnomad4 AMR
AF:
0.0521
Gnomad4 ASJ
AF:
0.0708
Gnomad4 EAS
AF:
0.00174
Gnomad4 SAS
AF:
0.0323
Gnomad4 FIN
AF:
0.166
Gnomad4 NFE
AF:
0.0988
Gnomad4 OTH
AF:
0.0730
Alfa
AF:
0.0869
Hom.:
855
Bravo
AF:
0.0622
Asia WGS
AF:
0.0140
AC:
47
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
2.8
DANN
Benign
0.79

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: rs13278559; hg19: chr8-86295423; API