7-91026725-G-T

Variant names:

• chr7-91026725-G-T
• rs10488001
• NM_001287135.2:c.1042-19172G>T

Variant summary

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

The NM_001287135.2(CDK14):​c.1042-19172G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,214 control chromosomes in the GnomAD database, including 409 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 0.065 (409 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.1042-19172G>T		intron_variant	Intron 10 of 14	ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.988-19172G>T		intron_variant	Intron 9 of 13		NP_036527.1
CDK14	NM_001287136.1	c.904-19172G>T		intron_variant	Intron 9 of 13		NP_001274065.1
CDK14	NM_001287137.1	c.655-19172G>T		intron_variant	Intron 8 of 12		NP_001274066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.1042-19172G>T		intron_variant	Intron 10 of 14	1	NM_001287135.2	ENSP00000369390.3
CDK14	ENST00000265741.7	c.988-19172G>T		intron_variant	Intron 9 of 13	1		ENSP00000265741.3
CDK14	ENST00000406263.5	c.904-19172G>T		intron_variant	Intron 9 of 13	1		ENSP00000385034.1
CDK14	ENST00000436577.3	c.655-19172G>T		intron_variant	Intron 8 of 12	2		ENSP00000398936.2

Frequencies

GnomAD3 genomes AF: 0.0651 AC: 9901 AN: 152096 Hom.: 408 Cov.: 32

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0651 AC: 9902 AN: 152214 Hom.: 409 Cov.: 32 AF XY: 0.0640 AC XY: 4760 AN XY: 74428

African (AFR) AF: 0.0262 AC: 1090 AN: 41534

American (AMR) AF: 0.0630 AC: 964 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0583 AC: 281 AN: 4818

European-Finnish (FIN) AF: 0.0586 AC: 621 AN: 10596

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0911 AC: 6194 AN: 68002

Other (OTH) AF: 0.0739 AC: 156 AN: 2110

Alfa AF: 0.0806 Hom.: 1204

Bravo AF: 0.0638

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		-0.077
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: rs10488001; hg19: chr7-90656040;