NM_020178.5:c.137-3277A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020178.5(CA10):​c.137-3277A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,928 control chromosomes in the GnomAD database, including 35,267 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 0.68 ( 35267 hom., cov: 31)

Consequence

CA10
NM_020178.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0130

Publications

7 publications found
Variant links:
Genes affected
CA10 (HGNC:1369): (carbonic anhydrase 10) This gene encodes a protein that belongs to the carbonic anhydrase family of zinc metalloenzymes, which catalyze the reversible hydration of carbon dioxide in various biological processes. The protein encoded by this gene is an acatalytic member of the alpha-carbonic anhydrase subgroup, and it is thought to play a role in the central nervous system, especially in brain development. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CA10NM_020178.5 linkc.137-3277A>C intron_variant Intron 2 of 8 ENST00000451037.7 NP_064563.1 Q9NS85-1A0A384MTY8
CA10NM_001082533.1 linkc.137-3277A>C intron_variant Intron 3 of 9 NP_001076002.1 Q9NS85-1A0A384MTY8
CA10NM_001082534.2 linkc.137-3277A>C intron_variant Intron 3 of 9 NP_001076003.1 Q9NS85-1A0A384MTY8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CA10ENST00000451037.7 linkc.137-3277A>C intron_variant Intron 2 of 8 1 NM_020178.5 ENSP00000405388.2 Q9NS85-1

Frequencies

GnomAD3 genomes
AF:
0.678
AC:
102977
AN:
151810
Hom.:
35255
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.649
Gnomad AMI
AF:
0.808
Gnomad AMR
AF:
0.635
Gnomad ASJ
AF:
0.748
Gnomad EAS
AF:
0.511
Gnomad SAS
AF:
0.647
Gnomad FIN
AF:
0.696
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.713
Gnomad OTH
AF:
0.697
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.678
AC:
103031
AN:
151928
Hom.:
35267
Cov.:
31
AF XY:
0.673
AC XY:
49992
AN XY:
74242
show subpopulations
African (AFR)
AF:
0.648
AC:
26852
AN:
41434
American (AMR)
AF:
0.634
AC:
9662
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
0.748
AC:
2598
AN:
3472
East Asian (EAS)
AF:
0.511
AC:
2622
AN:
5136
South Asian (SAS)
AF:
0.647
AC:
3112
AN:
4810
European-Finnish (FIN)
AF:
0.696
AC:
7348
AN:
10562
Middle Eastern (MID)
AF:
0.677
AC:
199
AN:
294
European-Non Finnish (NFE)
AF:
0.713
AC:
48433
AN:
67966
Other (OTH)
AF:
0.696
AC:
1468
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1649
3298
4948
6597
8246
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
818
1636
2454
3272
4090
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.680
Hom.:
4579
Bravo
AF:
0.667
Asia WGS
AF:
0.577
AC:
2006
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.90
DANN
Benign
0.55
PhyloP100
-0.013
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs203096; hg19: chr17-50011769; API