chr1-7256076-A-G

Position:

• chr1-7256076-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015215.4(CAMTA1):​c.438+6450A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,046 control chromosomes in the GnomAD database, including 43,680 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 0.75 (43680 hom., cov: 31)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.438+6450A>G		intron_variant		ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.438+6450A>G		intron_variant		1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114551 AN: 151928 Hom.: 43624 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.754 AC: 114664 AN: 152046 Hom.: 43680 Cov.: 31 AF XY: 0.752 AC XY: 55895 AN XY: 74322

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.745

Alfa AF: 0.729 Hom.: 23299

Bravo AF: 0.756

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.28

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

Publications

LitVar

Other links and lift over

dbSNP: rs7547519; hg19: chr1-7316136;