Variant rs200318010 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_015215.4(CAMTA1):c.806-5del variant causes a splice region, splice polypyrimidine tract, 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, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.23

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1063 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMTA1	NM_015215.4 linkuse as main transcript	c.806-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000303635.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMTA1	ENST00000303635.12 linkuse as main transcript	c.806-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_015215.4	P2	Q9Y6Y1-1

Frequencies

GnomAD3 genomes

AF:

0.00699

AC:

1064

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00713

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0240

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0103

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.00854

AC:

1558

AN:

182490

Hom.:

AF XY:

0.00931

AC XY:

893

AN XY:

95896

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00553

Gnomad ASJ exome

AF:

0.00366

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0219

Gnomad FIN exome

AF:

0.00337

Gnomad NFE exome

AF:

0.0110

Gnomad OTH exome

AF:

0.0102

GnomAD4 exome

AF:

0.00917

AC:

12546

AN:

1367458

Hom.:

107

Cov.:

AF XY:

0.00974

AC XY:

6514

AN XY:

668838

show subpopulations

Gnomad4 AFR exome

AF:

0.00144

Gnomad4 AMR exome

AF:

0.00576

Gnomad4 ASJ exome

AF:

0.00490

Gnomad4 EAS exome

AF:

0.0000775

Gnomad4 SAS exome

AF:

0.0245

Gnomad4 FIN exome

AF:

0.00403

Gnomad4 NFE exome

AF:

0.00907

Gnomad4 OTH exome

AF:

0.00887

GnomAD4 genome

AF:

0.00698

AC:

1063

AN:

152332

Hom.:

Cov.:

AF XY:

0.00718

AC XY:

535

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00712

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0238

Gnomad4 FIN

AF:

0.00358

Gnomad4 NFE

AF:

0.0103

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.00864

Hom.:

Bravo

AF:

0.00657

Asia WGS

AF:

0.00722

AC:

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

Benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	May 17, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 20, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over