rs975004

Variant names:

• chr7-90971314-A-G
• rs975004
• NM_001287135.2:c.948-12834A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-90971314-A-G
• chr7-90971314-A-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.948-12834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,208 control chromosomes in the GnomAD database, including 453 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 0.070 (453 hom., cov: 30)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.948-12834A>G		intron_variant	Intron 9 of 14	ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.894-12834A>G		intron_variant	Intron 8 of 13		NP_036527.1
CDK14	NM_001287136.1	c.810-12834A>G		intron_variant	Intron 8 of 13		NP_001274065.1
CDK14	NM_001287137.1	c.561-12834A>G		intron_variant	Intron 7 of 12		NP_001274066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.948-12834A>G		intron_variant	Intron 9 of 14	1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10680 AN: 152090 Hom.: 453 Cov.: 30

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0702 AC: 10684 AN: 152208 Hom.: 453 Cov.: 30 AF XY: 0.0721 AC XY: 5363 AN XY: 74422

African (AFR) AF: 0.0801 AC: 3328 AN: 41524

American (AMR) AF: 0.0941 AC: 1439 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.178 AC: 916 AN: 5160

South Asian (SAS) AF: 0.103 AC: 498 AN: 4828

European-Finnish (FIN) AF: 0.0600 AC: 637 AN: 10614

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0494 AC: 3358 AN: 68006

Other (OTH) AF: 0.0776 AC: 164 AN: 2114

Alfa AF: 0.0582 Hom.: 486

Bravo AF: 0.0728

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.53
PhyloP100		0.76
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: rs975004; hg19: chr7-90600629;