rs11120989

chr1-7617010-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.511-23390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,146 control chromosomes in the GnomAD database, including 6,981 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 0.24 (6981 hom., cov: 33)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMTA1	NM_015215.4	c.511-23390A>G		intron_variant		ENST00000303635.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMTA1	ENST00000303635.12	c.511-23390A>G		intron_variant		1	NM_015215.4	P2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36927 AN: 152028 Hom.: 6949 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.243 AC: 37012 AN: 152146 Hom.: 6981 Cov.: 33 AF XY: 0.239 AC XY: 17759 AN XY: 74396

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.217

Alfa AF: 0.198 Hom.: 1202

Bravo AF: 0.259

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.9
Dann	Benign	0.25

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: rs11120989; hg19: chr1-7677070;