17-20895774-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000327925.6(CCDC144NL):​n.384G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00731 in 1,613,506 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0075 ( 44 hom. )

Consequence

CCDC144NL
ENST00000327925.6 non_coding_transcript_exon

Scores

1
14

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.121
Variant links:
Genes affected
CCDC144NL-AS1 (HGNC:51340): (CCDC144NL antisense RNA 1)
CCDC144NL (HGNC:33735): (CCDC144A N-terminal like (pseudogene))

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.007117778).
BP6
Variant 17-20895774-C-T is Benign according to our data. Variant chr17-20895774-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2647571.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC144NLNR_164128.1 linkn.390G>A non_coding_transcript_exon_variant Exon 1 of 4
CCDC144NL-AS1NR_104185.2 linkn.362+3342C>T intron_variant Intron 2 of 2
CCDC144NL-AS1NR_160710.1 linkn.620+3342C>T intron_variant Intron 3 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC144NLENST00000327925.6 linkn.384G>A non_coding_transcript_exon_variant Exon 1 of 4 1
CCDC144NL-AS1ENST00000583962.2 linkn.369+3342C>T intron_variant Intron 2 of 2 1
CCDC144NLENST00000647562.3 linkn.247G>A non_coding_transcript_exon_variant Exon 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.00524
AC:
797
AN:
152154
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00155
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00616
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00476
Gnomad FIN
AF:
0.00677
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00780
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.00489
AC:
1226
AN:
250756
Hom.:
5
AF XY:
0.00514
AC XY:
697
AN XY:
135634
show subpopulations
Gnomad AFR exome
AF:
0.00131
Gnomad AMR exome
AF:
0.00234
Gnomad ASJ exome
AF:
0.000794
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00369
Gnomad FIN exome
AF:
0.00596
Gnomad NFE exome
AF:
0.00753
Gnomad OTH exome
AF:
0.00311
GnomAD4 exome
AF:
0.00753
AC:
10999
AN:
1461234
Hom.:
44
Cov.:
33
AF XY:
0.00744
AC XY:
5407
AN XY:
726936
show subpopulations
Gnomad4 AFR exome
AF:
0.00126
Gnomad4 AMR exome
AF:
0.00226
Gnomad4 ASJ exome
AF:
0.000804
Gnomad4 EAS exome
AF:
0.000202
Gnomad4 SAS exome
AF:
0.00391
Gnomad4 FIN exome
AF:
0.00627
Gnomad4 NFE exome
AF:
0.00880
Gnomad4 OTH exome
AF:
0.00590
GnomAD4 genome
AF:
0.00524
AC:
798
AN:
152272
Hom.:
4
Cov.:
32
AF XY:
0.00518
AC XY:
386
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.00154
Gnomad4 AMR
AF:
0.00621
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.00477
Gnomad4 FIN
AF:
0.00677
Gnomad4 NFE
AF:
0.00781
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00658
Hom.:
1
Bravo
AF:
0.00487
ESP6500AA
AF:
0.00159
AC:
7
ESP6500EA
AF:
0.00886
AC:
76
ExAC
AF:
0.00460
AC:
559
EpiCase
AF:
0.00720
EpiControl
AF:
0.00741

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Feb 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

CCDC144NL: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Benign
-0.65
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
4.1
DANN
Benign
0.94
DEOGEN2
Benign
0.0016
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.0092
N
LIST_S2
Benign
0.63
T
M_CAP
Benign
0.0017
T
MetaRNN
Benign
0.0071
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.22
N
PrimateAI
Uncertain
0.54
T
Polyphen
0.33
B
ClinPred
0.0016
T
GERP RS
-1.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.036
gMVP
0.14

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: rs150947349; hg19: chr17-20799087; API