rs6662747

Variant names:

• chr1-7662441-A-G
• rs6662747
• NM_015215.4:c.805+575A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-7662441-A-G
• chr1-7662441-A-T

Variant summary

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

The NM_015215.4(CAMTA1):​c.805+575A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,742 control chromosomes in the GnomAD database, including 17,454 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 0.48 (17454 hom., cov: 31)
• Consequence: CAMTA1 NM_015215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMTA1	NM_015215.4	c.805+575A>G		intron_variant	Intron 8 of 22	ENST00000303635.12	NP_056030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMTA1	ENST00000303635.12	c.805+575A>G		intron_variant	Intron 8 of 22	1	NM_015215.4	ENSP00000306522.6

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72220 AN: 151626 Hom.: 17420 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.477 AC: 72310 AN: 151742 Hom.: 17454 Cov.: 31 AF XY: 0.479 AC XY: 35509 AN XY: 74136

African (AFR) AF: 0.524 AC: 21681 AN: 41396

American (AMR) AF: 0.476 AC: 7247 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3464

East Asian (EAS) AF: 0.345 AC: 1775 AN: 5138

South Asian (SAS) AF: 0.398 AC: 1900 AN: 4776

European-Finnish (FIN) AF: 0.518 AC: 5458 AN: 10532

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31470 AN: 67888

Other (OTH) AF: 0.454 AC: 956 AN: 2106

Alfa AF: 0.459 Hom.: 26983

Bravo AF: 0.474

Asia WGS AF: 0.388 AC: 1354 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.16
PhyloP100		0.30
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: rs6662747; hg19: chr1-7722501;