GeneBe

rs15680

Variant names:

Variant summary

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

The ENST00000399751.7(LINC00680):​n.1589G>T 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 0.00000659 in 151,804 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 30)

Consequence

LINC00680
ENST00000399751.7 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0760

Publications

3 publications found
Variant links:
Genes affected
LINC00680 (HGNC:44417): (long intergenic non-protein coding RNA 680)
LINC00680-GUSBP4 (HGNC:56755): (LINC00680-GUSBP4 readthrough, transcribed pseudogene) This locus represents naturally-occurring readthrough transcription between the neighboring LINC00680 (long intergenic non-protein coding RNA 680) and GUSBP4 (glucuronidase, beta pseudogene 4) genes on chromosome 6. The readthrough transcript is unlikely to encode a protein. [provided by RefSeq, Oct 2015]

Genome browser will be placed here

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=-0.87).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00680NR_125727.1 linkn.1652G>T non_coding_transcript_exon_variant Exon 6 of 6
LINC00680NR_125728.1 linkn.1499G>T non_coding_transcript_exon_variant Exon 5 of 5
LINC00680NR_125729.1 linkn.1454G>T non_coding_transcript_exon_variant Exon 5 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00680ENST00000399751.7 linkn.1589G>T non_coding_transcript_exon_variant Exon 6 of 6 1
LINC00680ENST00000450081.6 linkn.1509G>T non_coding_transcript_exon_variant Exon 5 of 5 1
LINC00680ENST00000418368.2 linkn.1649G>T non_coding_transcript_exon_variant Exon 6 of 6 2

Frequencies

GnomAD3 genomes
AF:
0.00000659
AC:
1
AN:
151804
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
AF:
0.00000659
AC:
1
AN:
151804
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
74118
show subpopulations
African (AFR)
AF:
0.0000242
AC:
1
AN:
41298
American (AMR)
AF:
0.00
AC:
0
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5170
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4818
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10540
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67958
Other (OTH)
AF:
0.00
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
1668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
2.5
DANN
Benign
0.47
PhyloP100
0.076

Splicing

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

Publications

Other links and lift over

dbSNP: rs15680; hg19: chr6-58272436; API