NM_001379270.1:c.545+23_545+28delTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001379270.1(CNGA1):c.545+23_545+28delTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000257 in 1,165,676 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 0.0000078 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000019 ( 0 hom. )
Consequence
CNGA1
NM_001379270.1 intron
NM_001379270.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.04
Publications
3 publications found
Genes affected
CNGA1 (HGNC:2148): (cyclic nucleotide gated channel subunit alpha 1) The protein encoded by this gene is involved in phototransduction. Along with another protein, the encoded protein forms a cGMP-gated cation channel in the plasma membrane, allowing depolarization of rod photoreceptors. This represents the last step in the phototransduction pathway. Defects in this gene are a cause of retinitis pigmentosa autosomal recessive (ARRP) disease. Multiple transcript variants have been found for this gene. [provided by RefSeq, Oct 2019]
NIPAL1 (HGNC:27194): (NIPA like domain containing 1) Predicted to enable magnesium ion transmembrane transporter activity. Predicted to be involved in magnesium ion transport. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001379270.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CNGA1 | TSL:5 MANE Select | c.545+23_545+28delTTTTTT | intron | N/A | ENSP00000426862.3 | P29973 | |||
| CNGA1 | TSL:1 | c.545+23_545+28delTTTTTT | intron | N/A | ENSP00000384264.5 | P29973 | |||
| CNGA1 | TSL:2 | c.545+23_545+28delTTTTTT | intron | N/A | ENSP00000389881.3 | P29973 |
Frequencies
GnomAD3 genomes 0.00000784 AC: 1AN: 127606Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
127606
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000193 AC: 2AN: 1038070Hom.: 0 AF XY: 0.00000189 AC XY: 1AN XY: 528544 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
2
AN:
1038070
Hom.:
AF XY:
AC XY:
1
AN XY:
528544
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
22680
American (AMR)
AF:
AC:
0
AN:
33774
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21736
East Asian (EAS)
AF:
AC:
0
AN:
33496
South Asian (SAS)
AF:
AC:
0
AN:
67674
European-Finnish (FIN)
AF:
AC:
0
AN:
38450
Middle Eastern (MID)
AF:
AC:
0
AN:
3870
European-Non Finnish (NFE)
AF:
AC:
2
AN:
771174
Other (OTH)
AF:
AC:
0
AN:
45216
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000784 AC: 1AN: 127606Hom.: 0 Cov.: 0 AF XY: 0.0000163 AC XY: 1AN XY: 61218 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
127606
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
61218
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
34002
American (AMR)
AF:
AC:
0
AN:
12672
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3058
East Asian (EAS)
AF:
AC:
0
AN:
4462
South Asian (SAS)
AF:
AC:
0
AN:
3984
European-Finnish (FIN)
AF:
AC:
0
AN:
7098
Middle Eastern (MID)
AF:
AC:
0
AN:
266
European-Non Finnish (NFE)
AF:
AC:
0
AN:
59570
Other (OTH)
AF:
AC:
0
AN:
1702
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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