rs4905848

Variant summary

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

The NM_001144995.2(CCDC85C):​c.867+5578C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,016 control chromosomes in the GnomAD database, including 16,928 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 0.47 ( 16928 hom., cov: 32)

Consequence

CCDC85C
NM_001144995.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.94
Variant links:
Genes affected
CCDC85C (HGNC:35459): (coiled-coil domain containing 85C) Predicted to be involved in cerebral cortex development. Located in adherens junction. [provided by Alliance of Genome Resources, Apr 2022]
CCNK (HGNC:1596): (cyclin K) The protein encoded by this gene is a member of the transcription cyclin family. These cyclins may regulate transcription through their association with and activation of cyclin-dependent kinases (CDK) that phosphorylate the C-terminal domain (CTD) of the large subunit of RNA polymerase II. This gene product may play a dual role in regulating CDK and RNA polymerase II activities. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC85CNM_001144995.2 linkuse as main transcriptc.867+5578C>T intron_variant ENST00000380243.9 NP_001138467.1
CCDC85CXM_011536706.3 linkuse as main transcriptc.868-2181C>T intron_variant XP_011535008.1
CCDC85CXM_011536707.3 linkuse as main transcriptc.868-2181C>T intron_variant XP_011535009.1
CCDC85CXM_047431328.1 linkuse as main transcriptc.868-4157C>T intron_variant XP_047287284.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC85CENST00000380243.9 linkuse as main transcriptc.867+5578C>T intron_variant 5 NM_001144995.2 ENSP00000369592 P1

Frequencies

GnomAD3 genomes
AF:
0.466
AC:
70774
AN:
151898
Hom.:
16922
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.352
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.587
Gnomad ASJ
AF:
0.497
Gnomad EAS
AF:
0.536
Gnomad SAS
AF:
0.594
Gnomad FIN
AF:
0.430
Gnomad MID
AF:
0.484
Gnomad NFE
AF:
0.499
Gnomad OTH
AF:
0.483
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.466
AC:
70800
AN:
152016
Hom.:
16928
Cov.:
32
AF XY:
0.467
AC XY:
34720
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.352
Gnomad4 AMR
AF:
0.587
Gnomad4 ASJ
AF:
0.497
Gnomad4 EAS
AF:
0.537
Gnomad4 SAS
AF:
0.594
Gnomad4 FIN
AF:
0.430
Gnomad4 NFE
AF:
0.499
Gnomad4 OTH
AF:
0.485
Alfa
AF:
0.475
Hom.:
2177
Bravo
AF:
0.474
Asia WGS
AF:
0.522
AC:
1817
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.72
DANN
Benign
0.75

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: rs4905848; hg19: chr14-99996774; API