NM_153498.4:c.*1994A>G

Variant names:

• chr10-12830881-A-G
• rs2431623
• NM_153498.4:c.*1994A>G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 6 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153498.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	NM_153498.4	MANE Select	c.*1994A>G		3_prime_UTR	Exon 11 of 11	NP_705718.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	ENST00000619168.5	TSL:1 MANE Select	c.*1994A>G		3_prime_UTR	Exon 11 of 11	ENSP00000478874.1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 59302 AN: 149736 Hom.: 11863 Cov.: 28

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.: 68 Cov.: 0 AF XY: 0.261 AC XY: 245 AN XY: 940

African (AFR) AF: 0.286 AC: 8 AN: 28

American (AMR) AF: 0.167 AC: 3 AN: 18

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14

East Asian (EAS) AF: 0.176 AC: 6 AN: 34

South Asian (SAS) AF: 0.286 AC: 8 AN: 28

European-Finnish (FIN) AF: 0.353 AC: 12 AN: 34

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.265 AC: 277 AN: 1046

Other (OTH) AF: 0.231 AC: 12 AN: 52

GnomAD4 genome AF: 0.396 AC: 59341 AN: 149852 Hom.: 11881 Cov.: 28 AF XY: 0.397 AC XY: 28953 AN XY: 72972

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.091
DANN	Benign	0.44
PhyloP100		-2.7
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: rs2431623; hg19: chr10-12872880;