1-7509542-C-T

Variant names:

• chr1-7509542-C-T
• rs1193179
• NM_015215.4:c.510+41641C>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015215.4(CAMTA1):​c.510+41641C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,118 control chromosomes in the GnomAD database, including 31,273 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 0.63 (31273 hom., cov: 33)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.510+41641C>T		intron_variant	Intron 6 of 22	ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.510+41641C>T		intron_variant	Intron 6 of 22	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95040 AN: 152000 Hom.: 31257 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.625 AC: 95096 AN: 152118 Hom.: 31273 Cov.: 33 AF XY: 0.627 AC XY: 46599 AN XY: 74368

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.656

Alfa AF: 0.715 Hom.: 57027

Bravo AF: 0.600

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.62

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: rs1193179; hg19: chr1-7569602;