rs10489141

chr1-7193009-A-G

Variant summary

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

The NM_015215.4(CAMTA1):c.303-56482A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,090 control chromosomes in the GnomAD database, including 2,242 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 0.10 (2242 hom., cov: 32)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMTA1	NM_015215.4	c.303-56482A>G		intron_variant		ENST00000303635.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMTA1	ENST00000303635.12	c.303-56482A>G		intron_variant		1	NM_015215.4	P2

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15211 AN: 151972 Hom.: 2236 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.0809

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00551

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.100 AC: 15253 AN: 152090 Hom.: 2242 Cov.: 32 AF XY: 0.0966 AC XY: 7180 AN XY: 74356

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.0383

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.0807

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.00236

Gnomad4 NFE AF: 0.00552

Gnomad4 OTH AF: 0.0754

Alfa AF: 0.0593 Hom.: 172

Bravo AF: 0.114

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.065
Dann	Benign	0.62

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: rs10489141; hg19: chr1-7253069;