chr7-91128921-A-G

Variant names:

• chr7-91128921-A-G
• rs10488004
• NM_001287135.2:c.*28+10713A>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.*28+10713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,046 control chromosomes in the GnomAD database, including 27,855 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 0.56 (27855 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 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.*28+10713A>G		intron	N/A	NP_001274064.1
	CDK14	NM_012395.3		c.*28+10713A>G		intron	N/A	NP_036527.1
	CDK14	NM_001287136.1		c.*28+10713A>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.*28+10713A>G		intron	N/A	ENSP00000369390.3
	CDK14	ENST00000265741.7	TSL:1	c.*28+10713A>G		intron	N/A	ENSP00000265741.3
	CDK14	ENST00000406263.5	TSL:1	c.*28+10713A>G		intron	N/A	ENSP00000385034.1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85879 AN: 151928 Hom.: 27857 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.565 AC: 85888 AN: 152046 Hom.: 27855 Cov.: 32 AF XY: 0.562 AC XY: 41794 AN XY: 74314

African (AFR) AF: 0.239 AC: 9912 AN: 41486

American (AMR) AF: 0.541 AC: 8259 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2330 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2410 AN: 5150

South Asian (SAS) AF: 0.512 AC: 2468 AN: 4816

European-Finnish (FIN) AF: 0.720 AC: 7614 AN: 10578

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50707 AN: 67964

Other (OTH) AF: 0.575 AC: 1217 AN: 2116

Alfa AF: 0.678 Hom.: 115148

Bravo AF: 0.541

Asia WGS AF: 0.474 AC: 1643 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.58
PhyloP100		-1.1
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: rs10488004; hg19: chr7-90758236;