rs16831763

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_135570.1(LINC02049):​n.89+10139T>C 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 0.0306 in 152,300 control chromosomes in the GnomAD database, including 303 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 0.031 ( 303 hom., cov: 32)

Consequence

LINC02049
NR_135570.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.23).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02049NR_135570.1 linkuse as main transcriptn.89+10139T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000661060.1 linkuse as main transcriptn.947-13442T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0305
AC:
4641
AN:
152182
Hom.:
296
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00606
Gnomad AMI
AF:
0.0428
Gnomad AMR
AF:
0.161
Gnomad ASJ
AF:
0.0118
Gnomad EAS
AF:
0.0536
Gnomad SAS
AF:
0.0773
Gnomad FIN
AF:
0.0385
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0107
Gnomad OTH
AF:
0.0272
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0306
AC:
4655
AN:
152300
Hom.:
303
Cov.:
32
AF XY:
0.0356
AC XY:
2649
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.00606
Gnomad4 AMR
AF:
0.162
Gnomad4 ASJ
AF:
0.0118
Gnomad4 EAS
AF:
0.0538
Gnomad4 SAS
AF:
0.0769
Gnomad4 FIN
AF:
0.0385
Gnomad4 NFE
AF:
0.0107
Gnomad4 OTH
AF:
0.0265
Alfa
AF:
0.0386
Hom.:
67
Bravo
AF:
0.0375
Asia WGS
AF:
0.0790
AC:
273
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.23
CADD
Benign
17
DANN
Benign
0.82

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: rs16831763; hg19: chr3-120544977; API