rs4951291
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000418245.5(LINC00303):n.482A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: 𝑓 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LINC00303
ENST00000418245.5 non_coding_transcript_exon
ENST00000418245.5 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.280
Publications
11 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LINC00303 | NR_027902.2 | n.432+51A>T | intron_variant | Intron 3 of 5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LINC00303 | ENST00000418245.5 | n.482A>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 1 | |||||
| LINC00303 | ENST00000427799.1 | n.432+51A>T | intron_variant | Intron 3 of 5 | 1 | |||||
| LINC00303 | ENST00000367207.7 | n.483A>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 2 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 152080Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
0
AN:
152080
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 363716Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 208802
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
363716
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
208802
African (AFR)
AF:
AC:
0
AN:
10288
American (AMR)
AF:
AC:
0
AN:
35480
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11630
East Asian (EAS)
AF:
AC:
0
AN:
13140
South Asian (SAS)
AF:
AC:
0
AN:
66190
European-Finnish (FIN)
AF:
AC:
0
AN:
18016
Middle Eastern (MID)
AF:
AC:
0
AN:
1446
European-Non Finnish (NFE)
AF:
AC:
0
AN:
191158
Other (OTH)
AF:
AC:
0
AN:
16368
GnomAD4 genome 0.00 AC: 0AN: 152198Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74394
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
152198
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74394
African (AFR)
AF:
AC:
0
AN:
41538
American (AMR)
AF:
AC:
0
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5176
South Asian (SAS)
AF:
AC:
0
AN:
4816
European-Finnish (FIN)
AF:
AC:
0
AN:
10572
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68020
Other (OTH)
AF:
AC:
0
AN:
2116
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.