2-14167405-A-G

Variant summary

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

The ENST00000417751.5(LINC00276):​n.256+149564T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,458 control chromosomes in the GnomAD database, including 34,963 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 0.68 ( 34963 hom., cov: 32)

Consequence

LINC00276
ENST00000417751.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.315
Variant links:
Genes affected
LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 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
LINC00276ENST00000417751.5 linkn.256+149564T>C intron_variant Intron 2 of 4 2

Frequencies

GnomAD3 genomes
AF:
0.675
AC:
102228
AN:
151340
Hom.:
34936
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.589
Gnomad AMI
AF:
0.755
Gnomad AMR
AF:
0.621
Gnomad ASJ
AF:
0.669
Gnomad EAS
AF:
0.626
Gnomad SAS
AF:
0.651
Gnomad FIN
AF:
0.727
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.738
Gnomad OTH
AF:
0.637
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.675
AC:
102308
AN:
151458
Hom.:
34963
Cov.:
32
AF XY:
0.673
AC XY:
49792
AN XY:
73990
show subpopulations
Gnomad4 AFR
AF:
0.589
Gnomad4 AMR
AF:
0.621
Gnomad4 ASJ
AF:
0.669
Gnomad4 EAS
AF:
0.625
Gnomad4 SAS
AF:
0.653
Gnomad4 FIN
AF:
0.727
Gnomad4 NFE
AF:
0.738
Gnomad4 OTH
AF:
0.637
Alfa
AF:
0.725
Hom.:
38883
Bravo
AF:
0.665
Asia WGS
AF:
0.659
AC:
2282
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
8.2
DANN
Benign
0.85

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: rs1839206; hg19: chr2-14307530; API