rs2301461

Variant names:

• chr1-7329917-T-C
• rs2301461
• NM_015215.4:c.438+80291T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-7329917-T-C
• chr1-7329917-T-G

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+80291T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,084 control chromosomes in the GnomAD database, including 42,686 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 0.74 (42686 hom., cov: 33)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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+80291T>C		intron	N/A	NP_056030.1	Q9Y6Y1-1
	CAMTA1	NM_001349608.2		c.348+80291T>C		intron	N/A	NP_001336537.1
	CAMTA1	NM_001349609.2		c.438+80291T>C		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+80291T>C		intron	N/A	ENSP00000306522.6	Q9Y6Y1-1
	CAMTA1	ENST00000476864.2	TSL:1	c.438+80291T>C		intron	N/A	ENSP00000452319.2	A0A0C4DGL0
	CAMTA1	ENST00000700415.1		c.348+80291T>C		intron	N/A	ENSP00000514979.1	A0A8V8TQ65

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112651 AN: 151966 Hom.: 42628 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.741 AC: 112764 AN: 152084 Hom.: 42686 Cov.: 33 AF XY: 0.739 AC XY: 54904 AN XY: 74322

African (AFR) AF: 0.883 AC: 36665 AN: 41520

American (AMR) AF: 0.777 AC: 11862 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2632 AN: 3468

East Asian (EAS) AF: 0.842 AC: 4355 AN: 5170

South Asian (SAS) AF: 0.723 AC: 3476 AN: 4810

European-Finnish (FIN) AF: 0.591 AC: 6240 AN: 10562

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45245 AN: 67962

Other (OTH) AF: 0.755 AC: 1597 AN: 2116

Alfa AF: 0.683 Hom.: 16848

Bravo AF: 0.762

Asia WGS AF: 0.789 AC: 2747 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	0.27
DANN	Benign	0.60
PhyloP100		-2.1
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: rs2301461; hg19: chr1-7389977;