Variant chr3-9757429-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.183

Variant links:

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]

CAMK1 links:

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]

OGG1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CAMK1	NM_003656.5 linkuse as main transcript	c.*110T>C		3_prime_UTR_variant	12/12	ENST00000256460.8
OGG1	NM_002542.6 linkuse as main transcript			downstream_gene_variant		ENST00000344629.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK1	ENST00000256460.8 linkuse as main transcript	c.*110T>C		3_prime_UTR_variant	12/12	1	NM_003656.5	P1
OGG1	ENST00000344629.12 linkuse as main transcript			downstream_gene_variant		1	NM_002542.6	P1	O15527-1

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32475

AN:

152058

Hom.:

3952

Cov.:

show subpopulations

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.:

AF XY:

0.176

AC XY:

127361

AN XY:

723038

show subpopulations

Gnomad4 AFR exome

AF:

0.321

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.0980

Gnomad4 EAS exome

AF:

0.0485

Gnomad4 SAS exome

AF:

0.139

Gnomad4 FIN exome

AF:

0.239

Gnomad4 NFE exome

AF:

0.183

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.213

AC:

32483

AN:

152176

Hom.:

3953

Cov.:

AF XY:

0.212

AC XY:

15790

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.317

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.0432

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.190

Alfa

AF:

0.180

Hom.:

2944

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over