rs7547519

Variant names:

• chr1-7256076-A-G
• rs7547519
• NM_015215.4:c.438+6450A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-7256076-A-G
• chr1-7256076-A-T

Variant summary

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

The NM_015215.4(CAMTA1):​c.438+6450A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,046 control chromosomes in the GnomAD database, including 43,680 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 0.75 (43680 hom., cov: 31)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 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.438+6450A>G		intron	N/A	NP_056030.1
	CAMTA1	NM_001349608.2		c.348+6450A>G		intron	N/A	NP_001336537.1
	CAMTA1	NM_001349609.2		c.438+6450A>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.438+6450A>G		intron	N/A	ENSP00000306522.6
	CAMTA1	ENST00000476864.2	TSL:1	c.438+6450A>G		intron	N/A	ENSP00000452319.2
	CAMTA1	ENST00000700415.1		c.348+6450A>G		intron	N/A	ENSP00000514979.1

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114551 AN: 151928 Hom.: 43624 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.754 AC: 114664 AN: 152046 Hom.: 43680 Cov.: 31 AF XY: 0.752 AC XY: 55895 AN XY: 74322

African (AFR) AF: 0.855 AC: 35463 AN: 41484

American (AMR) AF: 0.699 AC: 10683 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2569 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3078 AN: 5158

South Asian (SAS) AF: 0.689 AC: 3319 AN: 4820

European-Finnish (FIN) AF: 0.736 AC: 7764 AN: 10546

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49271 AN: 67976

Other (OTH) AF: 0.745 AC: 1572 AN: 2110

Alfa AF: 0.730 Hom.: 25677

Bravo AF: 0.756

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.28
PhyloP100		-0.21
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: rs7547519; hg19: chr1-7316136;