chr1-7765251-G-A

Position:

• chr1-7765251-G-A

Variant summary

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

The NM_015215.4(CAMTA1):​c.4990-1208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,946 control chromosomes in the GnomAD database, including 20,867 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 0.51 (20867 hom., cov: 32)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.4990-1208G>A		intron_variant		ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.4990-1208G>A		intron_variant		1	NM_015215.4	ENSP00000306522	P2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77815 AN: 151828 Hom.: 20858 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.512 AC: 77868 AN: 151946 Hom.: 20867 Cov.: 32 AF XY: 0.510 AC XY: 37882 AN XY: 74258

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.488

Alfa AF: 0.451 Hom.: 32593

Bravo AF: 0.533

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.75

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: rs707455; hg19: chr1-7825311;