17-20895995-C-T
Variant names:
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
ENST00000327925.6 non_coding_transcript_exon
Scores
1
13
Clinical Significance
Conservation
PhyloP100: 0.246
Genes affected
CCDC144NL-AS1 (HGNC:51340): (CCDC144NL antisense RNA 1)
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC144NL | ENST00000327925.6 | n.163G>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | |||||
CCDC144NL-AS1 | ENST00000583962.2 | n.369+3563C>T | intron_variant | Intron 2 of 2 | 1 | |||||
CCDC144NL | ENST00000647562.3 | n.26G>A | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00743 AC: 1130AN: 152144Hom.: 23 Cov.: 32
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GnomAD3 exomes AF: 0.00225 AC: 557AN: 247822Hom.: 8 AF XY: 0.00168 AC XY: 226AN XY: 134162
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GnomAD4 exome AF: 0.00102 AC: 1487AN: 1457444Hom.: 23 Cov.: 34 AF XY: 0.000976 AC XY: 707AN XY: 724566
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GnomAD4 genome AF: 0.00745 AC: 1135AN: 152262Hom.: 23 Cov.: 32 AF XY: 0.00686 AC XY: 511AN XY: 74442
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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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PrimateAI
Benign
T
Polyphen
D
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