rs6865178

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001799.4(CDK7):​c.864+1089G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,034 control chromosomes in the GnomAD database, including 6,840 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 0.29 ( 6840 hom., cov: 32)

Consequence

CDK7
NM_001799.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360
Variant links:
Genes affected
CDK7 (HGNC:1778): (cyclin dependent kinase 7) The protein encoded by this gene is a member of the cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of Saccharomyces cerevisiae cdc28, and Schizosaccharomyces pombe cdc2, and are known to be important regulators of cell cycle progression. This protein forms a trimeric complex with cyclin H and MAT1, which functions as a Cdk-activating kinase (CAK). It is an essential component of the transcription factor TFIIH, that is involved in transcription initiation and DNA repair. This protein is thought to serve as a direct link between the regulation of transcription and the cell cycle. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDK7NM_001799.4 linkuse as main transcriptc.864+1089G>A intron_variant ENST00000256443.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDK7ENST00000256443.8 linkuse as main transcriptc.864+1089G>A intron_variant 1 NM_001799.4 P1

Frequencies

GnomAD3 genomes
AF:
0.286
AC:
43445
AN:
151918
Hom.:
6836
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.139
Gnomad AMI
AF:
0.526
Gnomad AMR
AF:
0.345
Gnomad ASJ
AF:
0.272
Gnomad EAS
AF:
0.424
Gnomad SAS
AF:
0.373
Gnomad FIN
AF:
0.348
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.333
Gnomad OTH
AF:
0.295
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.286
AC:
43457
AN:
152034
Hom.:
6840
Cov.:
32
AF XY:
0.289
AC XY:
21430
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.139
Gnomad4 AMR
AF:
0.346
Gnomad4 ASJ
AF:
0.272
Gnomad4 EAS
AF:
0.425
Gnomad4 SAS
AF:
0.372
Gnomad4 FIN
AF:
0.348
Gnomad4 NFE
AF:
0.333
Gnomad4 OTH
AF:
0.297
Alfa
AF:
0.319
Hom.:
5625
Bravo
AF:
0.279
Asia WGS
AF:
0.372
AC:
1290
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
11
DANN
Benign
0.83

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6865178; hg19: chr5-68569957; COSMIC: COSV56512692; COSMIC: COSV56512692; API