chr1-7193009-A-G

Variant names:

• chr1-7193009-A-G
• rs10489141
• NM_015215.4:c.303-56482A>G

Variant summary

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

The NM_015215.4(CAMTA1):​c.303-56482A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,090 control chromosomes in the GnomAD database, including 2,242 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 0.10 (2242 hom., cov: 32)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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.303-56482A>G		intron	N/A	NP_056030.1
	CAMTA1	NM_001349608.2		c.213-56482A>G		intron	N/A	NP_001336537.1
	CAMTA1	NM_001349609.2		c.303-56482A>G		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.303-56482A>G		intron	N/A	ENSP00000306522.6
	CAMTA1	ENST00000476864.2	TSL:1	c.303-56482A>G		intron	N/A	ENSP00000452319.2
	CAMTA1	ENST00000700415.1		c.213-56482A>G		intron	N/A	ENSP00000514979.1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15211 AN: 151972 Hom.: 2236 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.0809

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00551

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.100 AC: 15253 AN: 152090 Hom.: 2242 Cov.: 32 AF XY: 0.0966 AC XY: 7180 AN XY: 74356

African (AFR) AF: 0.327 AC: 13563 AN: 41458

American (AMR) AF: 0.0383 AC: 585 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 40 AN: 3470

East Asian (EAS) AF: 0.0807 AC: 416 AN: 5154

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4814

European-Finnish (FIN) AF: 0.00236 AC: 25 AN: 10608

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00552 AC: 375 AN: 67990

Other (OTH) AF: 0.0754 AC: 159 AN: 2110

Alfa AF: 0.0591 Hom.: 173

Bravo AF: 0.114

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.62
PhyloP100		-1.6
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: rs10489141; hg19: chr1-7253069;