1-6955045-T-C

Variant names:

• chr1-6955045-T-C
• rs884736
• NM_015215.4:c.234+129835T>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.234+129835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,794 control chromosomes in the GnomAD database, including 29,953 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 0.62 (29953 hom., cov: 30)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 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 = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.234+129835T>C		intron_variant	Intron 3 of 22	ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.234+129835T>C		intron_variant	Intron 3 of 22	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94289 AN: 151676 Hom.: 29916 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.622 AC: 94377 AN: 151794 Hom.: 29953 Cov.: 30 AF XY: 0.627 AC XY: 46520 AN XY: 74172

African (AFR) AF: 0.733 AC: 30294 AN: 41352

American (AMR) AF: 0.549 AC: 8379 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2044 AN: 3466

East Asian (EAS) AF: 0.825 AC: 4243 AN: 5140

South Asian (SAS) AF: 0.691 AC: 3318 AN: 4800

European-Finnish (FIN) AF: 0.614 AC: 6484 AN: 10558

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37785 AN: 67922

Other (OTH) AF: 0.592 AC: 1247 AN: 2106

Alfa AF: 0.573 Hom.: 22415

Bravo AF: 0.618

Asia WGS AF: 0.767 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.46
PhyloP100		0.026
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: rs884736; hg19: chr1-7015105;