rs10864294

Variant names:

• chr1-7333260-C-T
• rs10864294
• NM_015215.4:c.438+83634C>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+83634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,062 control chromosomes in the GnomAD database, including 4,035 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 0.18 (4035 hom., cov: 32)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• 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-IT1 (HGNC:41446): (CAMTA1 intronic transcript 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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.438+83634C>T		intron	N/A	NP_056030.1	Q9Y6Y1-1
	CAMTA1	NM_001349608.2		c.348+83634C>T		intron	N/A	NP_001336537.1
	CAMTA1	NM_001349609.2		c.438+83634C>T		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.438+83634C>T		intron	N/A	ENSP00000306522.6	Q9Y6Y1-1
	CAMTA1	ENST00000476864.2	TSL:1	c.438+83634C>T		intron	N/A	ENSP00000452319.2	A0A0C4DGL0
	CAMTA1	ENST00000700415.1		c.348+83634C>T		intron	N/A	ENSP00000514979.1	A0A8V8TQ65

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27565 AN: 151944 Hom.: 4017 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.0828

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.182 AC: 27633 AN: 152062 Hom.: 4035 Cov.: 32 AF XY: 0.180 AC XY: 13366 AN XY: 74348

African (AFR) AF: 0.409 AC: 16971 AN: 41444

American (AMR) AF: 0.144 AC: 2193 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.0417 AC: 216 AN: 5174

South Asian (SAS) AF: 0.0835 AC: 403 AN: 4826

European-Finnish (FIN) AF: 0.108 AC: 1145 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0828 AC: 5626 AN: 67968

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.171 Hom.: 686

Bravo AF: 0.195

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.62
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: rs10864294; hg19: chr1-7393320; COSMIC: COSV57889392;