rs34335657

Variant names:

• chr1-7767843-CAAA-C
• rs34335657
• ENST00000490905.5:c.*1332_*1334delAAA

Your query was ambiguous. Multiple possible variants found:

• chr1-7767843-CAAA-C
• chr1-7767843-CAAA-CA
• chr1-7767843-CAAA-CAA
• chr1-7767843-CAAA-CAAAA
• chr1-7767843-CAAA-CAAAAA
• chr1-7767843-CAAA-CAAAAAA
• chr1-7767843-CAAA-CAAAAAAA
• chr1-7767843-CAAA-CAAAAAAAA
• chr1-7767843-CAAA-CAAAAAAAAA
• chr1-7767843-CAAA-CAAAAAAAAAAA
• chr1-7767843-CAAA-CAAAAAAAAAAAAAA

Variant summary

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

The ENST00000490905.5(CAMTA1):​c.*1332_*1334delAAA variant causes a splice region change. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CAMTA1 ENST00000490905.5 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.06
• Publications: 0 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), Ambry Genetics, G2P, Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490905.5. 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.*1363_*1365delAAA		3_prime_UTR	Exon 23 of 23	NP_056030.1	Q9Y6Y1-1
	CAMTA1	NM_001349608.2		c.*1363_*1365delAAA		3_prime_UTR	Exon 22 of 22	NP_001336537.1
	CAMTA1	NM_001349609.2		c.*1332_*1334delAAA		3_prime_UTR	Exon 23 of 23	NP_001336538.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMTA1	ENST00000490905.5	TSL:1	c.*1332_*1334delAAA		splice_region	Exon 6 of 6	ENSP00000452024.1	H0YJR7
	CAMTA1	ENST00000303635.12	TSL:1 MANE Select	c.*1363_*1365delAAA		3_prime_UTR	Exon 23 of 23	ENSP00000306522.6	Q9Y6Y1-1
	CAMTA1	ENST00000476864.2	TSL:1	c.*1332_*1334delAAA		3_prime_UTR	Exon 22 of 22	ENSP00000452319.2	A0A0C4DGL0

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 244 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 152

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: 0.00 AC: 0 AN: 222

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 Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.1

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: rs34335657; hg19: chr1-7827903;