rs707455

Variant names:

• chr1-7765251-G-A
• rs707455
• NM_015215.4:c.4990-1208G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-7765251-G-A
• chr1-7765251-G-C
• chr1-7765251-G-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.4990-1208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,946 control chromosomes in the GnomAD database, including 20,867 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 0.51 (20867 hom., cov: 32)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516
• Publications: 17 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMTA1	NM_015215.4	MANE Select	c.4990-1208G>A		intron	N/A	NP_056030.1
	CAMTA1	NM_001349608.2		c.4900-1208G>A		intron	N/A	NP_001336537.1
	CAMTA1	NM_001349609.2		c.4641-1208G>A		intron	N/A	NP_001336538.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMTA1	ENST00000303635.12	TSL:1 MANE Select	c.4990-1208G>A		intron	N/A	ENSP00000306522.6
	CAMTA1	ENST00000476864.2	TSL:1	c.4620-1208G>A		intron	N/A	ENSP00000452319.2
	CAMTA1	ENST00000490905.5	TSL:1	c.654-1208G>A		intron	N/A	ENSP00000452024.1

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77815 AN: 151828 Hom.: 20858 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.512 AC: 77868 AN: 151946 Hom.: 20867 Cov.: 32 AF XY: 0.510 AC XY: 37882 AN XY: 74258

African (AFR) AF: 0.654 AC: 27101 AN: 41448

American (AMR) AF: 0.547 AC: 8363 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1397 AN: 3472

East Asian (EAS) AF: 0.727 AC: 3763 AN: 5176

South Asian (SAS) AF: 0.438 AC: 2107 AN: 4808

European-Finnish (FIN) AF: 0.387 AC: 4069 AN: 10518

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29491 AN: 67934

Other (OTH) AF: 0.488 AC: 1026 AN: 2104

Alfa AF: 0.464 Hom.: 54355

Bravo AF: 0.533

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.75
PhyloP100		0.52
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: rs707455; hg19: chr1-7825311;