chr1-7767843-C-CA

Position:

• chr1-7767843-C-CA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015215.4(CAMTA1):​c.*1365dupA variant causes a 3 prime UTR change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.066 (844 hom., cov: 0)
  • Exomes 𝑓: 0.13 (2 hom.)
• Consequence: CAMTA1 NM_015215.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.*1365dupA		3_prime_UTR_variant	23/23	ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.*1365dupA		3_prime_UTR_variant	23/23	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.0654 AC: 8892 AN: 135958 Hom.: 841 Cov.: 0

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0237

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.00752

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.00769

Gnomad FIN AF: 0.00713

Gnomad MID AF: 0.0138

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0480

GnomAD4 exome AF: 0.134 AC: 32 AN: 238 Hom.: 2 Cov.: 0 AF XY: 0.115 AC XY: 17 AN XY: 148

Gnomad4 EAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.130

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0655 AC: 8912 AN: 135976 Hom.: 844 Cov.: 0 AF XY: 0.0651 AC XY: 4247 AN XY: 65270

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0297

Gnomad4 ASJ AF: 0.00752

Gnomad4 EAS AF: 0.0148

Gnomad4 SAS AF: 0.00726

Gnomad4 FIN AF: 0.00713

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34335657; hg19: chr1-7827903;