Variant 1-7252112-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015215.4(CAMTA1):c.438+2486C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,960 control chromosomes in the GnomAD database, including 24,318 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 0.56 ( 24318 hom., cov: 31)

Consequence

CAMTA1
NM_015215.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.68

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMTA1	NM_015215.4 link	c.438+2486C>T		intron_variant		ENST00000303635.12	NP_056030.1	Q9Y6Y1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12 link	c.438+2486C>T		intron_variant		1	NM_015215.4	ENSP00000306522.6		Q9Y6Y1-1

Frequencies

GnomAD3 genomes

AF:

0.562

AC:

85298

AN:

151842

Hom.:

24312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.645

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.511

Gnomad EAS

AF:

0.563

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.577

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.526

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.562

AC:

85340

AN:

151960

Hom.:

24318

Cov.:

AF XY:

0.560

AC XY:

41588

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.485

Gnomad4 AMR

AF:

0.539

Gnomad4 ASJ

AF:

0.511

Gnomad4 EAS

AF:

0.564

Gnomad4 SAS

AF:

0.594

Gnomad4 FIN

AF:

0.577

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.591

Hom.:

36518

Bravo

AF:

0.554

Asia WGS

AF:

0.580

AC:

2018

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.021

DANN

Benign

0.45

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over