Genetic Variant NM_015215.4:c.*1365dupA (chr1-7767843-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015215.4(CAMTA1):c.*1365dupA variant causes a 3 prime UTR change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.066 ( 844 hom., cov: 0)

Exomes 𝑓: 0.13 ( 2 hom. )

Consequence

CAMTA1
NM_015215.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.00

Publications

4 publications found

Variant links:

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]

CAMTA1 Gene-Disease associations (from GenCC):

cerebellar dysfunction with variable cognitive and behavioral abnormalities
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Orphanet

CAMTA1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015215.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CAMTA1	NM_015215.4	MANE Select	c.*1365dupA	3_prime_UTR	Exon 23 of 23	NP_056030.1	Q9Y6Y1-1
CAMTA1	NM_001349608.2		c.*1365dupA	3_prime_UTR	Exon 22 of 22	NP_001336537.1
CAMTA1	NM_001349609.2		c.*1334dupA	3_prime_UTR	Exon 23 of 23	NP_001336538.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CAMTA1	ENST00000303635.12	TSL:1 MANE Select	c.*1365dupA	3_prime_UTR	Exon 23 of 23	ENSP00000306522.6	Q9Y6Y1-1
CAMTA1	ENST00000476864.2	TSL:1	c.*1334dupA	3_prime_UTR	Exon 22 of 22	ENSP00000452319.2	A0A0C4DGL0
CAMTA1	ENST00000700448.1		c.*1365dupA	3_prime_UTR	Exon 7 of 7	ENSP00000514999.1	A0A8V8TR85

Frequencies

GnomAD3 genomes

AF:

0.0654

AC:

8892

AN:

135958

Hom.:

841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.0237

Gnomad AMR

AF:

0.0296

Gnomad ASJ

AF:

0.00752

Gnomad EAS

AF:

0.0147

Gnomad SAS

AF:

0.00769

Gnomad FIN

AF:

0.00713

Gnomad MID

AF:

0.0138

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.0480

GnomAD4 exome

AF:

0.134

AC:

AN:

238

Hom.:

Cov.:

AF XY:

0.115

AC XY:

AN XY:

148

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.150

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.130

AC:

AN:

216

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

⚠️ 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: 0.289

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

AF:

0.0655

AC:

8912

AN:

135976

Hom.:

844

Cov.:

AF XY:

0.0651

AC XY:

4247

AN XY:

65270

show subpopulations

African (AFR)

AF:

0.204

AC:

7509

AN:

36802

American (AMR)

AF:

0.0297

AC:

405

AN:

13618

Ashkenazi Jewish (ASJ)

AF:

0.00752

AC:

AN:

3324

East Asian (EAS)

AF:

0.0148

AC:

AN:

4796

South Asian (SAS)

AF:

0.00726

AC:

AN:

4268

European-Finnish (FIN)

AF:

0.00713

AC:

AN:

6592

Middle Eastern (MID)

AF:

0.0148

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.0112

AC:

709

AN:

63552

Other (OTH)

AF:

0.0476

AC:

AN:

1910

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

322

644

966

1288

1610

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.0

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over