rs1017920

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000655671.1(LINC00299):​n.49-26082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,236 control chromosomes in the GnomAD database, including 594 homozygotes. 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 0.071 ( 594 hom., cov: 31)

Consequence

LINC00299
ENST00000655671.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.695
Variant links:
Genes affected
LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00299ENST00000655671.1 linkn.49-26082C>T intron_variant Intron 1 of 6
LINC00299ENST00000661371.1 linkn.90-26082C>T intron_variant Intron 1 of 5
LINC00299ENST00000669954.1 linkn.175+2404C>T intron_variant Intron 1 of 7

Frequencies

GnomAD3 genomes
AF:
0.0712
AC:
10824
AN:
152118
Hom.:
592
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0172
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0917
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.275
Gnomad SAS
AF:
0.0859
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.0740
Gnomad OTH
AF:
0.0852
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0712
AC:
10842
AN:
152236
Hom.:
594
Cov.:
31
AF XY:
0.0753
AC XY:
5606
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0172
Gnomad4 AMR
AF:
0.0920
Gnomad4 ASJ
AF:
0.114
Gnomad4 EAS
AF:
0.275
Gnomad4 SAS
AF:
0.0862
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.0740
Gnomad4 OTH
AF:
0.0890
Alfa
AF:
0.0755
Hom.:
237
Bravo
AF:
0.0674
Asia WGS
AF:
0.186
AC:
645
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.8
DANN
Benign
0.39

Splicing

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: rs1017920; hg19: chr2-8559180; API