rs238228

Variant names:

• chr17-4975665-G-A
• rs238228
• NM_015099.4:c.1901-1165C>T

Variant summary

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

The NM_015099.4(CAMTA2):​c.1901-1165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,076 control chromosomes in the GnomAD database, including 51,622 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 0.82 (51622 hom., cov: 31)
• Consequence: CAMTA2 NM_015099.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

CAMTA2 (HGNC:18807): (calmodulin binding transcription activator 2) The protein encoded by this gene is a member of the calmodulin-binding transcription activator protein family. Members of this family share a common domain structure that consists of a transcription activation domain, a DNA-binding domain, and a calmodulin-binding domain. The encoded protein may be a transcriptional coactivator of genes involved in cardiac growth. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMTA2	NM_015099.4	c.1901-1165C>T		intron_variant	Intron 11 of 22	ENST00000348066.8	NP_055914.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMTA2	ENST00000348066.8	c.1901-1165C>T		intron_variant	Intron 11 of 22	1	NM_015099.4	ENSP00000321813.7

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124064 AN: 151958 Hom.: 51553 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.838

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.817 AC: 124199 AN: 152076 Hom.: 51622 Cov.: 31 AF XY: 0.806 AC XY: 59884 AN XY: 74334

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.828

Alfa AF: 0.799 Hom.: 24530

Bravo AF: 0.836

Asia WGS AF: 0.543 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.61

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: rs238228; hg19: chr17-4878960;