rs56181605

Variant names:

• chr17-82251406-G-A
• rs56181605
• NM_001893.6:c.858C>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001893.6(CSNK1D):​c.858C>T​(p.Tyr286Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,614,106 control chromosomes in the GnomAD database, including 173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0094 (8 hom., cov: 32)
  • Exomes 𝑓: 0.013 (165 hom.)
• Consequence: CSNK1D NM_001893.6 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.218
• Publications: 6 publications found

Genes affected

CSNK1D (HGNC:2452): (casein kinase 1 delta) This gene is a member of the casein kinase I (CKI) gene family whose members have been implicated in the control of cytoplasmic and nuclear processes, including DNA replication and repair. The encoded protein may also be involved in the regulation of apoptosis, circadian rhythm, microtubule dynamics, chromosome segregation, and p53-mediated effects on growth. The encoded protein is highly similar to the mouse and rat CK1 delta homologs. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]

SLC16A3 (HGNC:10924): (solute carrier family 16 member 3) Lactic acid and pyruvate transport across plasma membranes is catalyzed by members of the proton-linked monocarboxylate transporter (MCT) family, which has been designated solute carrier family-16. Each MCT appears to have slightly different substrate and inhibitor specificities and transport kinetics, which are related to the metabolic requirements of the tissues in which it is found. The MCTs, which include MCT1 (SLC16A1; MIM 600682) and MCT2 (SLC16A7; MIM 603654), are characterized by 12 predicted transmembrane domains (Price et al., 1998 [PubMed 9425115]).[supplied by OMIM, Mar 2008]

ENSG00000280407 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP6: Variant 17-82251406-G-A is Benign according to our data. Variant chr17-82251406-G-A is described in ClinVar as Benign. ClinVar VariationId is 3387900.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.218 with no splicing effect.
• BS2: High AC in GnomAd4 at 1429 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001893.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1D	NM_001893.6	MANE Select	c.858C>T	p.Tyr286Tyr	synonymous	Exon 6 of 9	NP_001884.2
	CSNK1D	NM_001363749.2		c.858C>T	p.Tyr286Tyr	synonymous	Exon 6 of 9	NP_001350678.1	H7BYT1
	CSNK1D	NM_139062.4		c.858C>T	p.Tyr286Tyr	synonymous	Exon 6 of 10	NP_620693.1	P48730-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1D	ENST00000314028.11	TSL:1 MANE Select	c.858C>T	p.Tyr286Tyr	synonymous	Exon 6 of 9	ENSP00000324464.6	P48730-1
	CSNK1D	ENST00000392334.7	TSL:1	c.858C>T	p.Tyr286Tyr	synonymous	Exon 6 of 10	ENSP00000376146.2	P48730-2
	CSNK1D	ENST00000580784.5	TSL:1	n.8C>T		non_coding_transcript_exon	Exon 1 of 6	ENSP00000463906.1	J3QQU8

Frequencies

GnomAD3 genomes AF: 0.00939 AC: 1429 AN: 152160 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00203

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.00563

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00782

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.00863

GnomAD2 exomes AF: 0.00994 AC: 2497 AN: 251312 AF XY: 0.0106

Gnomad AFR exome AF: 0.00240

Gnomad AMR exome AF: 0.00289

Gnomad ASJ exome AF: 0.00854

Gnomad EAS exome AF: 0.000218

Gnomad FIN exome AF: 0.00790

Gnomad NFE exome AF: 0.0148

Gnomad OTH exome AF: 0.0121

GnomAD4 exome AF: 0.0127 AC: 18506 AN: 1461828 Hom.: 165 Cov.: 31 AF XY: 0.0129 AC XY: 9358 AN XY: 727202

African (AFR) AF: 0.00245 AC: 82 AN: 33480

American (AMR) AF: 0.00322 AC: 144 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00869 AC: 227 AN: 26136

East Asian (EAS) AF: 0.000101 AC: 4 AN: 39700

South Asian (SAS) AF: 0.0123 AC: 1061 AN: 86250

European-Finnish (FIN) AF: 0.00929 AC: 496 AN: 53402

Middle Eastern (MID) AF: 0.0154 AC: 89 AN: 5766

European-Non Finnish (NFE) AF: 0.0141 AC: 15701 AN: 1111984

Other (OTH) AF: 0.0116 AC: 702 AN: 60392

GnomAD4 genome AF: 0.00938 AC: 1429 AN: 152278 Hom.: 8 Cov.: 32 AF XY: 0.00921 AC XY: 686 AN XY: 74460

African (AFR) AF: 0.00200 AC: 83 AN: 41550

American (AMR) AF: 0.00562 AC: 86 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4826

European-Finnish (FIN) AF: 0.00782 AC: 83 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0155 AC: 1056 AN: 68024

Other (OTH) AF: 0.00854 AC: 18 AN: 2108

Alfa AF: 0.0130 Hom.: 8

Bravo AF: 0.00857

Asia WGS AF: 0.00375 AC: 14 AN: 3478

EpiCase AF: 0.0136

EpiControl AF: 0.0147

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	8.0
DANN	Benign	0.93
PhyloP100		0.22
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=98/2	polymorphism

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: rs56181605; hg19: chr17-80209282; COSMIC: COSV53927783; COSMIC: COSV53927783;