7-90787863-A-G

Variant names:

• chr7-90787863-A-G
• rs1110457
• NM_001287135.2:c.465-2710A>G

Variant summary

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

The NM_001287135.2(CDK14):​c.465-2710A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,896 control chromosomes in the GnomAD database, including 15,234 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 0.44 (15234 hom., cov: 31)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 1 publications found

Genes affected

CDK14 (HGNC:8883): (cyclin dependent kinase 14) Enables cyclin binding activity and cyclin-dependent protein serine/threonine kinase activity. Involved in G2/M transition of mitotic cell cycle and regulation of canonical Wnt signaling pathway. Located in cytosol; nucleoplasm; and plasma membrane. Part of cytoplasmic cyclin-dependent protein kinase holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001287135.2. 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
	CDK14	NM_001287135.2	MANE Select	c.465-2710A>G		intron	N/A	NP_001274064.1
	CDK14	NM_012395.3		c.411-2710A>G		intron	N/A	NP_036527.1
	CDK14	NM_001287136.1		c.327-2710A>G		intron	N/A	NP_001274065.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	ENST00000380050.8	TSL:1 MANE Select	c.465-2710A>G		intron	N/A	ENSP00000369390.3
	CDK14	ENST00000265741.7	TSL:1	c.411-2710A>G		intron	N/A	ENSP00000265741.3
	CDK14	ENST00000406263.5	TSL:1	c.327-2710A>G		intron	N/A	ENSP00000385034.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66187 AN: 151778 Hom.: 15233 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.436 AC: 66211 AN: 151896 Hom.: 15234 Cov.: 31 AF XY: 0.443 AC XY: 32853 AN XY: 74214

African (AFR) AF: 0.447 AC: 18487 AN: 41398

American (AMR) AF: 0.526 AC: 8026 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3468

East Asian (EAS) AF: 0.816 AC: 4222 AN: 5172

South Asian (SAS) AF: 0.446 AC: 2147 AN: 4810

European-Finnish (FIN) AF: 0.471 AC: 4959 AN: 10526

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25723 AN: 67948

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.398 Hom.: 6495

Bravo AF: 0.443

Asia WGS AF: 0.589 AC: 2042 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.42
DANN	Benign	0.77
PhyloP100		-0.72
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: rs1110457; hg19: chr7-90417178;