dbSNP rs2431623: CAMK1D:c.*1994A>G (chr10-12830881-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153498.4(CAMK1D):c.*1994A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 149,852 control chromosomes in the GnomAD database, including 11,881 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 0.40 ( 11881 hom., cov: 28)

Exomes 𝑓: 0.26 ( 68 hom. )

Failed GnomAD Quality Control

Consequence

CAMK1D
NM_153498.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.71

Publications

6 publications found

Variant links:

Genes affected

CAMK1D (HGNC:19341): (calcium/calmodulin dependent protein kinase ID) This gene is a member of the calcium/calmodulin-dependent protein kinase 1 family, a subfamily of the serine/threonine kinases. The encoded protein is a component of the calcium-regulated calmodulin-dependent protein kinase cascade. It has been associated with multiple processes including regulation of granulocyte function, activation of CREB-dependent gene transcription, aldosterone synthesis, differentiation and activation of neutrophil cells, and apoptosis of erythroleukemia cells. Alternatively spliced transcript variants encoding different isoforms of this gene have been described. [provided by RefSeq, Jan 2015]

CAMK1D links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4 link	c.*1994A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5 link	c.*1994A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_153498.4	ENSP00000478874.1

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

59302

AN:

149736

Hom.:

11863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.458

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.360

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.259

AC:

326

AN:

1260

Hom.:

Cov.:

AF XY:

0.261

AC XY:

245

AN XY:

940

show subpopulations

African (AFR)

AF:

0.286

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.176

AC:

AN:

South Asian (SAS)

AF:

0.286

AC:

AN:

European-Finnish (FIN)

AF:

0.353

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.265

AC:

277

AN:

1046

Other (OTH)

AF:

0.231

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.396

AC:

59341

AN:

149852

Hom.:

11881

Cov.:

AF XY:

0.397

AC XY:

28953

AN XY:

72972

show subpopulations

African (AFR)

AF:

0.458

AC:

18590

AN:

40620

American (AMR)

AF:

0.370

AC:

5566

AN:

15034

Ashkenazi Jewish (ASJ)

AF:

0.299

AC:

1033

AN:

3452

East Asian (EAS)

AF:

0.283

AC:

1422

AN:

5020

South Asian (SAS)

AF:

0.488

AC:

2311

AN:

4732

European-Finnish (FIN)

AF:

0.385

AC:

3867

AN:

10048

Middle Eastern (MID)

AF:

0.418

AC:

122

AN:

292

European-Non Finnish (NFE)

AF:

0.375

AC:

25354

AN:

67672

Other (OTH)

AF:

0.355

AC:

739

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1759

3517

5276

7034

8793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.377

Hom.:

3177

Bravo

AF:

0.392

Asia WGS

AF:

0.353

AC:

1228

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.091

(source)

DANN

Benign

0.44

PhyloP100

-2.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over