2-41953045-T-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_161189.1(LINC02898):n.344A>G 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 0.000983 in 1,551,032 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00095 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00099 ( 1 hom. )
Consequence
LINC02898
NR_161189.1 non_coding_transcript_exon
NR_161189.1 non_coding_transcript_exon
Scores
14
Clinical Significance
Conservation
PhyloP100: 0.140
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0078119636).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC02898 | NR_161189.1 | n.344A>G | non_coding_transcript_exon_variant | 2/4 | ||||
LOC124905996 | XR_007086296.1 | n.613T>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC02898 | ENST00000378711.2 | n.341A>G | non_coding_transcript_exon_variant | 2/4 | 2 | |||||
LINC02898 | ENST00000403980.1 | n.515A>G | non_coding_transcript_exon_variant | 2/2 | 3 | |||||
LINC02898 | ENST00000615044.1 | n.251A>G | non_coding_transcript_exon_variant | 1/2 | 5 | |||||
LINC02898 | ENST00000649862.1 | n.582A>G | non_coding_transcript_exon_variant | 3/5 |
Frequencies
GnomAD3 genomes AF: 0.000953 AC: 145AN: 152194Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000686 AC: 104AN: 151634Hom.: 0 AF XY: 0.000740 AC XY: 60AN XY: 81114
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GnomAD4 exome AF: 0.000987 AC: 1381AN: 1398718Hom.: 1 Cov.: 31 AF XY: 0.00104 AC XY: 718AN XY: 689844
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GnomAD4 genome AF: 0.000945 AC: 144AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000765 AC XY: 57AN XY: 74490
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.251A>G (p.Q84R) alteration is located in exon 2 (coding exon 1) of the C2orf91 gene. This alteration results from a A to G substitution at nucleotide position 251, causing the glutamine (Q) at amino acid position 84 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
N
MVP
0.040
ClinPred
T
GERP RS
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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