chr1-7767843-C-CAA

Position:

• chr1-7767843-C-CAA

Variant summary

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

The NM_015215.4(CAMTA1):​c.*1364_*1365dupAA variant causes a 3 prime UTR change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.77 (39952 hom., cov: 0)
  • Exomes 𝑓: 0.61 (41 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 (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.*1364_*1365dupAA		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.*1364_*1365dupAA		3_prime_UTR_variant	23/23	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.766 AC: 104121 AN: 135924 Hom.: 39969 Cov.: 0

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.777

GnomAD4 exome AF: 0.607 AC: 147 AN: 242 Hom.: 41 Cov.: 0 AF XY: 0.600 AC XY: 90 AN XY: 150

Gnomad4 EAS exome AF: 0.350

Gnomad4 FIN exome AF: 0.632

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.766 AC: 104103 AN: 135940 Hom.: 39952 Cov.: 0 AF XY: 0.768 AC XY: 50139 AN XY: 65266

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.780

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;