rs200318010
Variant names:
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_015215.4(CAMTA1):c.806-5delC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00895 in 1,519,790 control chromosomes in the GnomAD database, including 110 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0070 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0092 ( 107 hom. )
Consequence
CAMTA1
NM_015215.4 splice_region, intron
NM_015215.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.23
Genes affected
CAMTA1 (HGNC:18806): (calmodulin binding transcription activator 1) The protein encoded by this gene contains a CG1 DNA-binding domain, a transcription factor immunoglobulin domain, ankyrin repeats, and calmodulin-binding IQ motifs. The encoded protein is thought to be a transcription factor and may be a tumor suppressor. However, a translocation event is sometimes observed between this gene and the WWTR1 gene, with the resulting WWTR1-CAMTA1 oncoprotein leading to epithelioid hemangioendothelioma, a malignant vascular cancer. [provided by RefSeq, Mar 2017]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP6
Variant 1-7663346-TC-T is Benign according to our data. Variant chr1-7663346-TC-T is described in ClinVar as [Benign]. Clinvar id is 235450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-7663346-TC-T is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00698 (1063/152332) while in subpopulation SAS AF = 0.0238 (115/4828). AF 95% confidence interval is 0.0203. There are 3 homozygotes in GnomAd4. There are 535 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position FAILED quality control check.
BS2
High AC in GnomAd4 at 1063 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00699 AC: 1064AN: 152214Hom.: 3 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1064
AN:
152214
Hom.:
Cov.:
33
Gnomad AFR
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GnomAD2 exomes AF: 0.00854 AC: 1558AN: 182490 AF XY: 0.00931 show subpopulations
GnomAD2 exomes
AF:
AC:
1558
AN:
182490
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.00917 AC: 12546AN: 1367458Hom.: 107 Cov.: 31 AF XY: 0.00974 AC XY: 6514AN XY: 668838 show subpopulations
GnomAD4 exome
AF:
AC:
12546
AN:
1367458
Hom.:
Cov.:
31
AF XY:
AC XY:
6514
AN XY:
668838
Gnomad4 AFR exome
AF:
AC:
44
AN:
30590
Gnomad4 AMR exome
AF:
AC:
179
AN:
31078
Gnomad4 ASJ exome
AF:
AC:
99
AN:
20190
Gnomad4 EAS exome
AF:
AC:
3
AN:
38724
Gnomad4 SAS exome
AF:
AC:
1746
AN:
71392
Gnomad4 FIN exome
AF:
AC:
200
AN:
49588
Gnomad4 NFE exome
AF:
AC:
9653
AN:
1064358
Gnomad4 Remaining exome
AF:
AC:
499
AN:
56226
Heterozygous variant carriers
0
703
1406
2110
2813
3516
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
346
692
1038
1384
1730
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome AF: 0.00698 AC: 1063AN: 152332Hom.: 3 Cov.: 33 AF XY: 0.00718 AC XY: 535AN XY: 74490 show subpopulations
GnomAD4 genome
AF:
AC:
1063
AN:
152332
Hom.:
Cov.:
33
AF XY:
AC XY:
535
AN XY:
74490
Gnomad4 AFR
AF:
AC:
0.00120227
AN:
0.00120227
Gnomad4 AMR
AF:
AC:
0.00712046
AN:
0.00712046
Gnomad4 ASJ
AF:
AC:
0.00460829
AN:
0.00460829
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.0238194
AN:
0.0238194
Gnomad4 FIN
AF:
AC:
0.00357546
AN:
0.00357546
Gnomad4 NFE
AF:
AC:
0.0102914
AN:
0.0102914
Gnomad4 OTH
AF:
AC:
0.013245
AN:
0.013245
Heterozygous variant carriers
0
60
120
181
241
301
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Variant carriers
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
25
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Jan 27, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
May 17, 2016
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mutation Taster
=100/0
polymorphism
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at