rs1476047

Variant names:

• chr1-7252112-C-T
• rs1476047
• NM_015215.4:c.438+2486C>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+2486C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,960 control chromosomes in the GnomAD database, including 24,318 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 0.56 (24318 hom., cov: 31)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.68
• Publications: 9 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.438+2486C>T		intron_variant	Intron 5 of 22	ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.438+2486C>T		intron_variant	Intron 5 of 22	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85298 AN: 151842 Hom.: 24312 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.562 AC: 85340 AN: 151960 Hom.: 24318 Cov.: 31 AF XY: 0.560 AC XY: 41588 AN XY: 74264

African (AFR) AF: 0.485 AC: 20075 AN: 41414

American (AMR) AF: 0.539 AC: 8236 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2914 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2858 AN: 4814

European-Finnish (FIN) AF: 0.577 AC: 6081 AN: 10536

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41573 AN: 67972

Other (OTH) AF: 0.526 AC: 1107 AN: 2106

Alfa AF: 0.588 Hom.: 45462

Bravo AF: 0.554

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.021
DANN	Benign	0.45
PhyloP100		-4.7
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: rs1476047; hg19: chr1-7312172; COSMIC: COSV57889112;