2-188280414-A-T

Variant summary

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

The NR_126396.1(LINC01090):​n.225+7053T>A 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 0.198 in 152,108 control chromosomes in the GnomAD database, including 3,621 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 0.20 ( 3621 hom., cov: 33)

Consequence

LINC01090
NR_126396.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600
Variant links:
Genes affected
LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01090NR_126396.1 linkuse as main transcriptn.225+7053T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01090ENST00000434418.2 linkuse as main transcriptn.225+7053T>A intron_variant, non_coding_transcript_variant 5
LINC01090ENST00000415357.1 linkuse as main transcriptn.168+7053T>A intron_variant, non_coding_transcript_variant 3
LINC01090ENST00000632331.1 linkuse as main transcriptn.81-91286T>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.198
AC:
30054
AN:
151990
Hom.:
3603
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.334
Gnomad AMI
AF:
0.157
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.110
Gnomad EAS
AF:
0.0512
Gnomad SAS
AF:
0.0725
Gnomad FIN
AF:
0.162
Gnomad MID
AF:
0.174
Gnomad NFE
AF:
0.156
Gnomad OTH
AF:
0.180
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.198
AC:
30135
AN:
152108
Hom.:
3621
Cov.:
33
AF XY:
0.194
AC XY:
14397
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.335
Gnomad4 AMR
AF:
0.152
Gnomad4 ASJ
AF:
0.110
Gnomad4 EAS
AF:
0.0513
Gnomad4 SAS
AF:
0.0719
Gnomad4 FIN
AF:
0.162
Gnomad4 NFE
AF:
0.156
Gnomad4 OTH
AF:
0.188
Alfa
AF:
0.181
Hom.:
369
Bravo
AF:
0.202
Asia WGS
AF:
0.105
AC:
363
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.5
DANN
Benign
0.25

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: rs6718697; hg19: chr2-189145141; API