1-7053052-G-C

Variant names:

• chr1-7053052-G-C
• rs11120822
• NM_015215.4:c.235-38252G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015215.4(CAMTA1):​c.235-38252G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,188 control chromosomes in the GnomAD database, including 9,625 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 0.34 (9625 hom., cov: 33)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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.235-38252G>C		intron	N/A	NP_056030.1
	CAMTA1	NM_001349608.2		c.145-38252G>C		intron	N/A	NP_001336537.1
	CAMTA1	NM_001349609.2		c.235-38252G>C		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.235-38252G>C		intron	N/A	ENSP00000306522.6
	CAMTA1	ENST00000476864.2	TSL:1	c.235-38252G>C		intron	N/A	ENSP00000452319.2
	CAMTA1	ENST00000700415.1		c.145-38252G>C		intron	N/A	ENSP00000514979.1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52371 AN: 152070 Hom.: 9626 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.344 AC: 52398 AN: 152188 Hom.: 9625 Cov.: 33 AF XY: 0.347 AC XY: 25813 AN XY: 74396

African (AFR) AF: 0.233 AC: 9696 AN: 41534

American (AMR) AF: 0.360 AC: 5509 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1239 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2693 AN: 5154

South Asian (SAS) AF: 0.342 AC: 1650 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4513 AN: 10592

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26091 AN: 68008

Other (OTH) AF: 0.345 AC: 728 AN: 2112

Alfa AF: 0.373 Hom.: 1354

Bravo AF: 0.337

Asia WGS AF: 0.402 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.70
PhyloP100		-0.031
Mutation Taster		=100/0	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: rs11120822; hg19: chr1-7113112;