2-8419050-G-A

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, non coding transcript 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, non_coding_transcript

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/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC00299ENST00000655671.1 linkuse as main transcriptn.49-26082C>T intron_variant, non_coding_transcript_variant
LINC00299ENST00000661371.1 linkuse as main transcriptn.90-26082C>T intron_variant, non_coding_transcript_variant
LINC00299ENST00000669954.1 linkuse as main transcriptn.175+2404C>T intron_variant, non_coding_transcript_variant

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