7-90631883-C-G

Variant names:

• chr7-90631883-C-G
• rs885972
• NM_001287135.2:c.123+27634C>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.123+27634C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,996 control chromosomes in the GnomAD database, including 7,762 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 0.30 (7762 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 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]

TVP23CP1 (HGNC:44646): (TVP23C pseudogene 1)

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 (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.123+27634C>G		intron_variant	Intron 2 of 14	ENST00000380050.8	NP_001274064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.123+27634C>G		intron_variant	Intron 2 of 14	1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45822 AN: 151848 Hom.: 7751 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.298

GnomAD4 exome AF: 0.333 AC: 10 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.318 AC XY: 7 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.321 AC: 9 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.302 AC: 45863 AN: 151966 Hom.: 7762 Cov.: 32 AF XY: 0.308 AC XY: 22914 AN XY: 74288

African (AFR) AF: 0.354 AC: 14660 AN: 41432

American (AMR) AF: 0.404 AC: 6168 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3466

East Asian (EAS) AF: 0.673 AC: 3469 AN: 5152

South Asian (SAS) AF: 0.381 AC: 1838 AN: 4824

European-Finnish (FIN) AF: 0.249 AC: 2631 AN: 10554

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15350 AN: 67962

Other (OTH) AF: 0.297 AC: 627 AN: 2110

Alfa AF: 0.264 Hom.: 745

Bravo AF: 0.320

Asia WGS AF: 0.491 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.69
DANN	Benign	0.53
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: rs885972; hg19: chr7-90261197;