chr17-82247837-A-G

Variant names:

• chr17-82247837-A-G
• rs4510078
• NM_001893.6:c.1197+1038T>C

Variant summary

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

The NM_001893.6(CSNK1D):​c.1197+1038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 985,452 control chromosomes in the GnomAD database, including 477,014 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 0.99 (74473 hom., cov: 33)
  • Exomes 𝑓: 0.98 (402541 hom.)
• Consequence: CSNK1D NM_001893.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1D	NM_001893.6	MANE Select	c.1197+1038T>C		intron	N/A	NP_001884.2
	CSNK1D	NM_001363749.2		c.1197+1038T>C		intron	N/A	NP_001350678.1
	CSNK1D	NM_139062.4		c.1197+1038T>C		intron	N/A	NP_620693.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1D	ENST00000314028.11	TSL:1 MANE Select	c.1197+1038T>C		intron	N/A	ENSP00000324464.6
	CSNK1D	ENST00000392334.7	TSL:1	c.1197+1038T>C		intron	N/A	ENSP00000376146.2
	CSNK1D	ENST00000580784.5	TSL:1	n.*769+1038T>C		intron	N/A	ENSP00000463906.1

Frequencies

GnomAD3 genomes AF: 0.989 AC: 150518 AN: 152228 Hom.: 74415 Cov.: 33

Gnomad AFR AF: 0.997

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.979

GnomAD4 exome AF: 0.983 AC: 818947 AN: 833106 Hom.: 402541 Cov.: 38 AF XY: 0.983 AC XY: 378183 AN XY: 384716

African (AFR) AF: 0.998 AC: 15759 AN: 15786

American (AMR) AF: 0.985 AC: 969 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 5097 AN: 5152

East Asian (EAS) AF: 1.00 AC: 3630 AN: 3630

South Asian (SAS) AF: 0.990 AC: 16299 AN: 16460

European-Finnish (FIN) AF: 0.996 AC: 277 AN: 278

Middle Eastern (MID) AF: 0.993 AC: 1608 AN: 1620

European-Non Finnish (NFE) AF: 0.982 AC: 748468 AN: 761898

Other (OTH) AF: 0.983 AC: 26840 AN: 27298

GnomAD4 genome AF: 0.989 AC: 150635 AN: 152346 Hom.: 74473 Cov.: 33 AF XY: 0.989 AC XY: 73677 AN XY: 74498

African (AFR) AF: 0.997 AC: 41466 AN: 41576

American (AMR) AF: 0.985 AC: 15068 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3442 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5188 AN: 5188

South Asian (SAS) AF: 0.992 AC: 4791 AN: 4828

European-Finnish (FIN) AF: 0.991 AC: 10527 AN: 10624

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66880 AN: 68038

Other (OTH) AF: 0.980 AC: 2073 AN: 2116

Alfa AF: 0.987 Hom.: 17489

Bravo AF: 0.989

Asia WGS AF: 0.997 AC: 3468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		0.0090
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: rs4510078; hg19: chr17-80205713;