ENST00000446107.2:n.60T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000446107.2(LINC00841):​n.60T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

LINC00841
ENST00000446107.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Publications

3 publications found
Variant links:
Genes affected
LINC00841 (HGNC:27430): (long intergenic non-protein coding RNA 841)
LINC02659 (HGNC:54145): (long intergenic non-protein coding RNA 2659)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00841NR_136148.1 linkn.48T>A non_coding_transcript_exon_variant Exon 1 of 2
LINC00841NR_033846.2 linkn.191+2790T>A intron_variant Intron 2 of 7
LINC00841NR_136147.1 linkn.191+2790T>A intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00841ENST00000446107.2 linkn.60T>A non_coding_transcript_exon_variant Exon 1 of 2 2
LINC00841ENST00000826345.1 linkn.40T>A non_coding_transcript_exon_variant Exon 1 of 3
LINC00841ENST00000826346.1 linkn.38T>A non_coding_transcript_exon_variant Exon 1 of 5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
264
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
176
African (AFR)
AF:
0.00
AC:
0
AN:
6
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
84
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
158
Other (OTH)
AF:
0.00
AC:
0
AN:
12
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.27
DANN
Benign
0.19
PhyloP100
-2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2274241; hg19: chr10-44407897; API