1-6876212-G-A

Variant names:

• chr1-6876212-G-A
• rs7546903
• NM_015215.4:c.234+51002G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015215.4(CAMTA1):​c.234+51002G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,142 control chromosomes in the GnomAD database, including 35,307 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 0.68 (35307 hom., cov: 28)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• 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 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.234+51002G>A		intron_variant	Intron 3 of 22	ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.234+51002G>A		intron_variant	Intron 3 of 22	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.679 AC: 102589 AN: 151024 Hom.: 35253 Cov.: 28

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.679 AC: 102693 AN: 151142 Hom.: 35307 Cov.: 28 AF XY: 0.677 AC XY: 49992 AN XY: 73822

African (AFR) AF: 0.631 AC: 25932 AN: 41086

American (AMR) AF: 0.773 AC: 11767 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2394 AN: 3456

East Asian (EAS) AF: 0.394 AC: 2015 AN: 5110

South Asian (SAS) AF: 0.606 AC: 2885 AN: 4758

European-Finnish (FIN) AF: 0.703 AC: 7320 AN: 10406

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48020 AN: 67818

Other (OTH) AF: 0.713 AC: 1493 AN: 2094

Alfa AF: 0.704 Hom.: 62838

Bravo AF: 0.680

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.023
DANN	Benign	0.63
PhyloP100		-0.96
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs7546903; hg19: chr1-6936272;