2-41953045-T-C

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

Scores

14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.140
Variant links:
Genes affected

Genome browser will be placed here

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
LINC02898NR_161189.1 linkuse as main transcriptn.344A>G non_coding_transcript_exon_variant 2/4
LOC124905996XR_007086296.1 linkuse as main transcriptn.613T>C non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02898ENST00000378711.2 linkuse as main transcriptn.341A>G non_coding_transcript_exon_variant 2/42
LINC02898ENST00000403980.1 linkuse as main transcriptn.515A>G non_coding_transcript_exon_variant 2/23
LINC02898ENST00000615044.1 linkuse as main transcriptn.251A>G non_coding_transcript_exon_variant 1/25
LINC02898ENST00000649862.1 linkuse as main transcriptn.582A>G non_coding_transcript_exon_variant 3/5

Frequencies

GnomAD3 genomes
AF:
0.000953
AC:
145
AN:
152194
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00105
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.000471
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00162
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.000686
AC:
104
AN:
151634
Hom.:
0
AF XY:
0.000740
AC XY:
60
AN XY:
81114
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000162
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00111
Gnomad FIN exome
AF:
0.000293
Gnomad NFE exome
AF:
0.00117
Gnomad OTH exome
AF:
0.000899
GnomAD4 exome
AF:
0.000987
AC:
1381
AN:
1398718
Hom.:
1
Cov.:
31
AF XY:
0.00104
AC XY:
718
AN XY:
689844
show subpopulations
Gnomad4 AFR exome
AF:
0.000127
Gnomad4 AMR exome
AF:
0.000364
Gnomad4 ASJ exome
AF:
0.0000397
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00110
Gnomad4 FIN exome
AF:
0.000351
Gnomad4 NFE exome
AF:
0.00111
Gnomad4 OTH exome
AF:
0.000928
GnomAD4 genome
AF:
0.000945
AC:
144
AN:
152314
Hom.:
0
Cov.:
32
AF XY:
0.000765
AC XY:
57
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.000168
Gnomad4 AMR
AF:
0.00105
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.000471
Gnomad4 NFE
AF:
0.00162
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00116
Hom.:
0
Bravo
AF:
0.000967
TwinsUK
AF:
0.00108
AC:
4
ALSPAC
AF:
0.000778
AC:
3
ExAC
AF:
0.000659
AC:
15
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

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 submitterclinical testingAmbry GeneticsAug 13, 2021The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.62
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
9.2
DANN
Benign
0.82
DEOGEN2
Benign
0.054
T;.
Eigen
Benign
-0.67
Eigen_PC
Benign
-0.80
FATHMM_MKL
Benign
0.020
N
LIST_S2
Benign
0.37
T;T
M_CAP
Benign
0.00096
T
MetaRNN
Benign
0.0078
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.0
N;.
MutationTaster
Benign
1.0
N
MVP
0.040
ClinPred
0.099
T
GERP RS
-0.55
Varity_R
0.49
gMVP
0.014

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs200161608; hg19: chr2-42180185; API