NM_153498.4:c.92+12389G>A

Variant names:

• chr10-12362299-G-A
• rs11257738
• NM_153498.4:c.92+12389G>A

Variant summary

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

The NM_153498.4(CAMK1D):​c.92+12389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,068 control chromosomes in the GnomAD database, including 2,557 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 0.11 (2557 hom., cov: 31)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 2 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.92+12389G>A		intron_variant	Intron 1 of 10	ENST00000619168.5	NP_705718.1
CAMK1D	NM_020397.4	c.92+12389G>A		intron_variant	Intron 1 of 9		NP_065130.1
CAMK1D	XM_006717482.4	c.92+12389G>A		intron_variant	Intron 1 of 10		XP_006717545.1
CAMK1D	XM_006717483.5	c.92+12389G>A		intron_variant	Intron 1 of 10		XP_006717546.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.92+12389G>A		intron_variant	Intron 1 of 10	1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.92+12389G>A		intron_variant	Intron 1 of 9	1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.259+12389G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16954 AN: 151950 Hom.: 2545 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.00643

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00864

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.112 AC: 16995 AN: 152068 Hom.: 2557 Cov.: 31 AF XY: 0.110 AC XY: 8196 AN XY: 74334

African (AFR) AF: 0.340 AC: 14081 AN: 41412

American (AMR) AF: 0.0595 AC: 909 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3472

East Asian (EAS) AF: 0.118 AC: 608 AN: 5168

South Asian (SAS) AF: 0.0991 AC: 477 AN: 4812

European-Finnish (FIN) AF: 0.00643 AC: 68 AN: 10582

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00863 AC: 587 AN: 68020

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0337 Hom.: 774

Bravo AF: 0.125

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.091
DANN	Benign	0.58
PhyloP100		-2.2
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: rs11257738; hg19: chr10-12404298;