17-20895774-C-T
Variant names:
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
ENST00000327925.6 non_coding_transcript_exon
Scores
1
14
Clinical Significance
Conservation
PhyloP100: -0.121
Genes affected
CCDC144NL-AS1 (HGNC:51340): (CCDC144NL antisense RNA 1)
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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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC144NL | ENST00000327925.6 | n.384G>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | |||||
CCDC144NL-AS1 | ENST00000583962.2 | n.369+3342C>T | intron_variant | Intron 2 of 2 | 1 | |||||
CCDC144NL | ENST00000647562.3 | n.247G>A | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00524 AC: 797AN: 152154Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00489 AC: 1226AN: 250756Hom.: 5 AF XY: 0.00514 AC XY: 697AN XY: 135634
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GnomAD4 exome AF: 0.00753 AC: 10999AN: 1461234Hom.: 44 Cov.: 33 AF XY: 0.00744 AC XY: 5407AN XY: 726936
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GnomAD4 genome AF: 0.00524 AC: 798AN: 152272Hom.: 4 Cov.: 32 AF XY: 0.00518 AC XY: 386AN XY: 74458
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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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Uncertain
T
Polyphen
B
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at