chr1-7767843-C-CAAA

Position:

• chr1-7767843-C-CAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_015215.4(CAMTA1):​c.*1363_*1365dupAAA variant causes a 3 prime UTR change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.047 (267 hom., cov: 0)
  • Exomes 𝑓: 0.029 (1 hom.)
  • Failed GnomAD Quality Control
• 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.*1363_*1365dupAAA		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.*1363_*1365dupAAA		3_prime_UTR_variant	23/23	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 6362 AN: 135910 Hom.: 267 Cov.: 0

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0154

Gnomad EAS AF: 0.00976

Gnomad SAS AF: 0.0324

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0448

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0417

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0292 AC: 7 AN: 240 Hom.: 1 Cov.: 0 AF XY: 0.0400 AC XY: 6 AN XY: 150

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0321

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0469 AC: 6370 AN: 135928 Hom.: 267 Cov.: 0 AF XY: 0.0468 AC XY: 3052 AN XY: 65252

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0154

Gnomad4 EAS AF: 0.00980

Gnomad4 SAS AF: 0.0324

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0413

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;