rs7546903

Positions:

• chr1-6876212-G-A
• chr1-6876212-G-C
• chr1-6876212-G-T

Variant summary

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

The NM_015215.4(CAMTA1):​c.234+51002G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,142 control chromosomes in the GnomAD database, including 35,307 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 0.68 (35307 hom., cov: 28)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMTA1	NM_015215.4	c.234+51002G>A		intron_variant		ENST00000303635.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMTA1	ENST00000303635.12	c.234+51002G>A		intron_variant		1	NM_015215.4	P2

Frequencies

GnomAD3 genomes AF: 0.679 AC: 102589 AN: 151024 Hom.: 35253 Cov.: 28

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.679 AC: 102693 AN: 151142 Hom.: 35307 Cov.: 28 AF XY: 0.677 AC XY: 49992 AN XY: 73822

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.713

Alfa AF: 0.704 Hom.: 49526

Bravo AF: 0.680

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.023
DANN	Benign	0.63
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs7546903; hg19: chr1-6936272;