rs6602595

Variant names:

• chr10-12549917-G-A
• rs6602595
• NM_153498.4:c.93-3308G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-12549917-G-A
• chr10-12549917-G-C

Variant summary

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

The NM_153498.4(CAMK1D):​c.93-3308G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,032 control chromosomes in the GnomAD database, including 22,227 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 0.53 (22227 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.93-3308G>A		intron_variant	Intron 1 of 10	ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.93-3308G>A		intron_variant	Intron 1 of 10	1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.93-3308G>A		intron_variant	Intron 1 of 9	1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.260-116819G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81226 AN: 151914 Hom.: 22227 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.534 AC: 81257 AN: 152032 Hom.: 22227 Cov.: 32 AF XY: 0.532 AC XY: 39506 AN XY: 74314

African (AFR) AF: 0.450 AC: 18656 AN: 41452

American (AMR) AF: 0.437 AC: 6677 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1954 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2401 AN: 5172

South Asian (SAS) AF: 0.485 AC: 2334 AN: 4810

European-Finnish (FIN) AF: 0.588 AC: 6211 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41137 AN: 67960

Other (OTH) AF: 0.542 AC: 1146 AN: 2114

Alfa AF: 0.582 Hom.: 18980

Bravo AF: 0.519

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.86
PhyloP100		0.23
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: rs6602595; hg19: chr10-12591916;