NM_001287135.2:c.1042-19172G>A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001287135.2(CDK14):​c.1042-19172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.1042-19172G>A		intron_variant	Intron 10 of 14	ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.988-19172G>A		intron_variant	Intron 9 of 13		NP_036527.1
CDK14	NM_001287136.1	c.904-19172G>A		intron_variant	Intron 9 of 13		NP_001274065.1
CDK14	NM_001287137.1	c.655-19172G>A		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>A		intron_variant	Intron 10 of 14	1	NM_001287135.2	ENSP00000369390.3
CDK14	ENST00000265741.7	c.988-19172G>A		intron_variant	Intron 9 of 13	1		ENSP00000265741.3
CDK14	ENST00000406263.5	c.904-19172G>A		intron_variant	Intron 9 of 13	1		ENSP00000385034.1
CDK14	ENST00000436577.3	c.655-19172G>A		intron_variant	Intron 8 of 12	2		ENSP00000398936.2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.76
PhyloP100		-0.077

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;