1-7767843-CA-C

Position:

• chr1-7767843-CA-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000490905.5(CAMTA1):​c.*1334delA variant causes a splice region change. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00034 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0082 (0 hom.)
• Consequence: CAMTA1 ENST00000490905.5 splice_region
• 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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000338 (46/136134) while in subpopulation AFR AF= 0.000516 (19/36828). AF 95% confidence interval is 0.000337. There are 0 homozygotes in gnomad4. There are 26 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 46 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.000338 AC: 46 AN: 136116 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000517

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000147

Gnomad ASJ AF: 0.00180

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000466

Gnomad FIN AF: 0.000303

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000236

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00820 AC: 2 AN: 244 Hom.: 0 Cov.: 0 AF XY: 0.00658 AC XY: 1 AN XY: 152

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00901

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000338 AC: 46 AN: 136134 Hom.: 0 Cov.: 0 AF XY: 0.000398 AC XY: 26 AN XY: 65360

Gnomad4 AFR AF: 0.000516

Gnomad4 AMR AF: 0.000147

Gnomad4 ASJ AF: 0.00180

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000469

Gnomad4 FIN AF: 0.000303

Gnomad4 NFE AF: 0.000236

Gnomad4 OTH AF: 0.00

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;