1-7767843-CAAA-CAAAAAA

Variant names:

• chr1-7767843-C-CAAA
• rs34335657
• NM_015215.4:c.*1363_*1365dupAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015215.4(CAMTA1):​c.*1363_*1365dupAAA variant causes a 3 prime UTR change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.047 (267 hom., cov: 0)
  • Exomes 𝑓: 0.029 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: CAMTA1 NM_015215.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00
• Publications: 4 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: Uncertain_significance. The variant received 0 ACMG points.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMTA1	NM_015215.4	MANE Select	c.*1363_*1365dupAAA		3_prime_UTR	Exon 23 of 23	NP_056030.1
	CAMTA1	NM_001349608.2		c.*1363_*1365dupAAA		3_prime_UTR	Exon 22 of 22	NP_001336537.1
	CAMTA1	NM_001349609.2		c.*1332_*1334dupAAA		3_prime_UTR	Exon 23 of 23	NP_001336538.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMTA1	ENST00000303635.12	TSL:1 MANE Select	c.*1363_*1365dupAAA		3_prime_UTR	Exon 23 of 23	ENSP00000306522.6
	CAMTA1	ENST00000476864.2	TSL:1	c.*1332_*1334dupAAA		3_prime_UTR	Exon 22 of 22	ENSP00000452319.2
	CAMTA1	ENST00000700448.1		c.*1363_*1365dupAAA		3_prime_UTR	Exon 7 of 7	ENSP00000514999.1

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 6362 AN: 135910 Hom.: 267 Cov.: 0

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0154

Gnomad EAS AF: 0.00976

Gnomad SAS AF: 0.0324

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0448

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0417

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0292 AC: 7 AN: 240 Hom.: 1 Cov.: 0 AF XY: 0.0400 AC XY: 6 AN XY: 150

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 20

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0321 AC: 7 AN: 218

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0469 AC: 6370 AN: 135928 Hom.: 267 Cov.: 0 AF XY: 0.0468 AC XY: 3052 AN XY: 65252

African (AFR) AF: 0.100 AC: 3677 AN: 36776

American (AMR) AF: 0.0325 AC: 443 AN: 13618

Ashkenazi Jewish (ASJ) AF: 0.0154 AC: 51 AN: 3322

East Asian (EAS) AF: 0.00980 AC: 47 AN: 4798

South Asian (SAS) AF: 0.0324 AC: 138 AN: 4260

European-Finnish (FIN) AF: 0.0308 AC: 203 AN: 6596

Middle Eastern (MID) AF: 0.0481 AC: 13 AN: 270

European-Non Finnish (NFE) AF: 0.0265 AC: 1684 AN: 63538

Other (OTH) AF: 0.0413 AC: 79 AN: 1912

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.0
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34335657; hg19: chr1-7827903;