chr3-9757429-A-G

Variant names:

• chr3-9757429-A-G
• rs293795
• NM_003656.5:c.*110T>C

Variant summary

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

The NM_003656.5(CAMK1):​c.*110T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,607,078 control chromosomes in the GnomAD database, including 28,121 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 0.21 (3953 hom., cov: 32)
  • Exomes 𝑓: 0.18 (24168 hom.)
• Consequence: CAMK1 NM_003656.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

Genes affected

CAMK1 (HGNC:1459): (calcium/calmodulin dependent protein kinase I) Calcium/calmodulin-dependent protein kinase I is expressed in many tissues and is a component of a calmodulin-dependent protein kinase cascade. Calcium/calmodulin directly activates calcium/calmodulin-dependent protein kinase I by binding to the enzyme and indirectly promotes the phosphorylation and synergistic activation of the enzyme by calcium/calmodulin-dependent protein kinase I kinase. [provided by RefSeq, Jul 2008]

OGG1 (HGNC:8125): (8-oxoguanine DNA glycosylase) This gene encodes the enzyme responsible for the excision of 8-oxoguanine, a mutagenic base byproduct which occurs as a result of exposure to reactive oxygen. The action of this enzyme includes lyase activity for chain cleavage. Alternative splicing of the C-terminal region of this gene classifies splice variants into two major groups, type 1 and type 2, depending on the last exon of the sequence. Type 1 alternative splice variants end with exon 7 and type 2 end with exon 8. All variants share the N-terminal region in common, which contains a mitochondrial targeting signal that is essential for mitochondrial localization. Many alternative splice variants for this gene have been described, but the full-length nature for every variant has not been determined. [provided by RefSeq, Aug 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1	NM_003656.5	c.*110T>C		3_prime_UTR_variant	Exon 12 of 12	ENST00000256460.8	NP_003647.1
OGG1	NM_002542.6	c.*279A>G		downstream_gene_variant		ENST00000344629.12	NP_002533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1	ENST00000256460	c.*110T>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_003656.5	ENSP00000256460.3
OGG1	ENST00000344629.12	c.*279A>G		downstream_gene_variant		1	NM_002542.6	ENSP00000342851.7

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32475 AN: 152058 Hom.: 3952 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.177 AC: 258093 AN: 1454902 Hom.: 24168 Cov.: 35 AF XY: 0.176 AC XY: 127361 AN XY: 723038

Gnomad4 AFR exome AF: 0.321 AC: 10714 AN: 33348

Gnomad4 AMR exome AF: 0.111 AC: 4835 AN: 43542

Gnomad4 ASJ exome AF: 0.0980 AC: 2543 AN: 25944

Gnomad4 EAS exome AF: 0.0485 AC: 1917 AN: 39506

Gnomad4 SAS exome AF: 0.139 AC: 11935 AN: 85732

Gnomad4 FIN exome AF: 0.239 AC: 12693 AN: 53058

Gnomad4 NFE exome AF: 0.183 AC: 203099 AN: 1107878

Gnomad4 Remaining exome AF: 0.164 AC: 9862 AN: 60170

GnomAD4 genome AF: 0.213 AC: 32483 AN: 152176 Hom.: 3953 Cov.: 32 AF XY: 0.212 AC XY: 15790 AN XY: 74426

Gnomad4 AFR AF: 0.317 AC: 0.316556 AN: 0.316556

Gnomad4 AMR AF: 0.156 AC: 0.156483 AN: 0.156483

Gnomad4 ASJ AF: 0.105 AC: 0.104551 AN: 0.104551

Gnomad4 EAS AF: 0.0432 AC: 0.0431599 AN: 0.0431599

Gnomad4 SAS AF: 0.139 AC: 0.139361 AN: 0.139361

Gnomad4 FIN AF: 0.235 AC: 0.234596 AN: 0.234596

Gnomad4 NFE AF: 0.187 AC: 0.186787 AN: 0.186787

Gnomad4 OTH AF: 0.190 AC: 0.190341 AN: 0.190341

Alfa AF: 0.185 Hom.: 4015

Bravo AF: 0.210

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.4
DANN	Benign	0.76
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

Publications

LitVar

Other links and lift over

dbSNP: rs293795; hg19: chr3-9799113; COSMIC: COSV56540400; COSMIC: COSV56540400;