rs6951213

Variant names:

• chr7-90783786-G-A
• rs6951213
• NM_001287135.2:c.465-6787G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-90783786-G-A
• chr7-90783786-G-C

Variant summary

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

The NM_001287135.2(CDK14):​c.465-6787G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,908 control chromosomes in the GnomAD database, including 15,199 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 (15199 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.465-6787G>A		intron_variant	Intron 4 of 14	ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.411-6787G>A		intron_variant	Intron 3 of 13		NP_036527.1
CDK14	NM_001287136.1	c.327-6787G>A		intron_variant	Intron 3 of 13		NP_001274065.1
CDK14	NM_001287137.1	c.78-6787G>A		intron_variant	Intron 2 of 12		NP_001274066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.465-6787G>A		intron_variant	Intron 4 of 14	1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66112 AN: 151790 Hom.: 15198 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.435 AC: 66137 AN: 151908 Hom.: 15199 Cov.: 32 AF XY: 0.443 AC XY: 32856 AN XY: 74244

African (AFR) AF: 0.444 AC: 18397 AN: 41426

American (AMR) AF: 0.525 AC: 8015 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3466

East Asian (EAS) AF: 0.818 AC: 4221 AN: 5162

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4820

European-Finnish (FIN) AF: 0.473 AC: 4990 AN: 10540

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

European-Non Finnish (NFE) AF: 0.379 AC: 25709 AN: 67922

Other (OTH) AF: 0.424 AC: 896 AN: 2112

Alfa AF: 0.437 Hom.: 2644

Bravo AF: 0.442

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.50
PhyloP100		0.36
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: rs6951213; hg19: chr7-90413101;