17-20895995-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000327925.6(CCDC144NL):​n.163G>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 0.00163 in 1,609,706 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0075 ( 23 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 23 hom. )

Consequence

CCDC144NL
ENST00000327925.6 non_coding_transcript_exon

Scores

1
13

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.246
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0043634176).
BP6
Variant 17-20895995-C-T is Benign according to our data. Variant chr17-20895995-C-T is described in ClinVar as [Benign]. Clinvar id is 709931.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00745 (1135/152262) while in subpopulation AFR AF= 0.0255 (1059/41524). AF 95% confidence interval is 0.0242. There are 23 homozygotes in gnomad4. There are 511 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 23 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC144NLNR_164128.1 linkn.169G>A non_coding_transcript_exon_variant Exon 1 of 4
CCDC144NL-AS1NR_104185.2 linkn.362+3563C>T intron_variant Intron 2 of 2
CCDC144NL-AS1NR_160710.1 linkn.620+3563C>T intron_variant Intron 3 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC144NLENST00000327925.6 linkn.163G>A non_coding_transcript_exon_variant Exon 1 of 4 1
CCDC144NL-AS1ENST00000583962.2 linkn.369+3563C>T intron_variant Intron 2 of 2 1
CCDC144NLENST00000647562.3 linkn.26G>A non_coding_transcript_exon_variant Exon 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.00743
AC:
1130
AN:
152144
Hom.:
23
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0255
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00216
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000265
Gnomad OTH
AF:
0.00814
GnomAD3 exomes
AF:
0.00225
AC:
557
AN:
247822
Hom.:
8
AF XY:
0.00168
AC XY:
226
AN XY:
134162
show subpopulations
Gnomad AFR exome
AF:
0.0280
Gnomad AMR exome
AF:
0.000991
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00220
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000896
Gnomad OTH exome
AF:
0.000332
GnomAD4 exome
AF:
0.00102
AC:
1487
AN:
1457444
Hom.:
23
Cov.:
34
AF XY:
0.000976
AC XY:
707
AN XY:
724566
show subpopulations
Gnomad4 AFR exome
AF:
0.0307
Gnomad4 AMR exome
AF:
0.00121
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000757
Gnomad4 SAS exome
AF:
0.00173
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000105
Gnomad4 OTH exome
AF:
0.00231
GnomAD4 genome
AF:
0.00745
AC:
1135
AN:
152262
Hom.:
23
Cov.:
32
AF XY:
0.00686
AC XY:
511
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.0255
Gnomad4 AMR
AF:
0.00216
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000265
Gnomad4 OTH
AF:
0.00806
Alfa
AF:
0.000334
Hom.:
0
Bravo
AF:
0.00844
ESP6500AA
AF:
0.0157
AC:
69
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.00290
AC:
352
Asia WGS
AF:
0.00318
AC:
11
AN:
3476
EpiCase
AF:
0.000109
EpiControl
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Apr 10, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.61
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
3.5
DANN
Uncertain
1.0
DEOGEN2
Benign
0.0023
T
Eigen
Benign
-0.52
Eigen_PC
Benign
-0.74
FATHMM_MKL
Benign
0.027
N
LIST_S2
Benign
0.68
T
MetaRNN
Benign
0.0044
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.90
L
PrimateAI
Benign
0.45
T
Polyphen
0.99
D
ClinPred
0.029
T
GERP RS
0.87
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.20
gMVP
0.041

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: rs111327075; hg19: chr17-20799308; API