rs7519687

Positions:

• chr1-7589655-G-A
• chr1-7589655-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015215.4(CAMTA1):​c.511-50745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,120 control chromosomes in the GnomAD database, including 4,504 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 0.21 (4504 hom., cov: 33)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.511-50745G>A		intron_variant		ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.511-50745G>A		intron_variant		1	NM_015215.4	ENSP00000306522	P2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31208 AN: 152002 Hom.: 4470 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.206 AC: 31286 AN: 152120 Hom.: 4504 Cov.: 33 AF XY: 0.203 AC XY: 15101 AN XY: 74382

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.185

Alfa AF: 0.134 Hom.: 2108

Bravo AF: 0.216

Asia WGS AF: 0.194 AC: 676 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	0.14
DANN	Benign	0.65

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

Other links and lift over

dbSNP: rs7519687; hg19: chr1-7649715;