1-7509542-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• cerebellar dysfunction with variable cognitive and behavioral abnormalities

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics, Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015215.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMTA1	NM_015215.4	MANE Select	c.510+41641C>T		intron	N/A	NP_056030.1
	CAMTA1	NM_001349608.2		c.420+41641C>T		intron	N/A	NP_001336537.1
	CAMTA1	NM_001349609.2		c.510+41641C>T		intron	N/A	NP_001336538.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMTA1	ENST00000303635.12	TSL:1 MANE Select	c.510+41641C>T		intron	N/A	ENSP00000306522.6
	CAMTA1	ENST00000476864.2	TSL:1	c.510+41641C>T		intron	N/A	ENSP00000452319.2
	CAMTA1	ENST00000700415.1		c.420+41641C>T		intron	N/A	ENSP00000514979.1

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

African (AFR) AF: 0.423 AC: 17526 AN: 41460

American (AMR) AF: 0.593 AC: 9076 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2550 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2549 AN: 5162

South Asian (SAS) AF: 0.671 AC: 3228 AN: 4814

European-Finnish (FIN) AF: 0.765 AC: 8116 AN: 10606

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49846 AN: 67992

Other (OTH) AF: 0.656 AC: 1387 AN: 2114

Alfa AF: 0.696 Hom.: 135124

Bravo AF: 0.600

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.62
PhyloP100		1.5
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1193179; hg19: chr1-7569602;