chr5-15169346-C-T

Variant summary

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

The ENST00000651224.1(LINC02149):​n.311+22923G>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 0.329 in 151,986 control chromosomes in the GnomAD database, including 8,653 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 0.33 ( 8653 hom., cov: 32)

Consequence

LINC02149
ENST00000651224.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0850
Variant links:
Genes affected
LINC02149 (HGNC:53010): (long intergenic non-protein coding RNA 2149)

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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC02149ENST00000651224.1 linkuse as main transcriptn.311+22923G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.329
AC:
50040
AN:
151868
Hom.:
8661
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.231
Gnomad AMI
AF:
0.366
Gnomad AMR
AF:
0.301
Gnomad ASJ
AF:
0.432
Gnomad EAS
AF:
0.170
Gnomad SAS
AF:
0.223
Gnomad FIN
AF:
0.377
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.401
Gnomad OTH
AF:
0.359
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.329
AC:
50042
AN:
151986
Hom.:
8653
Cov.:
32
AF XY:
0.324
AC XY:
24058
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.231
Gnomad4 AMR
AF:
0.300
Gnomad4 ASJ
AF:
0.432
Gnomad4 EAS
AF:
0.170
Gnomad4 SAS
AF:
0.223
Gnomad4 FIN
AF:
0.377
Gnomad4 NFE
AF:
0.401
Gnomad4 OTH
AF:
0.353
Alfa
AF:
0.363
Hom.:
1269
Bravo
AF:
0.318
Asia WGS
AF:
0.191
AC:
667
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
2.0
DANN
Benign
0.41

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: rs977762; hg19: chr5-15169455; COSMIC: COSV68636758; API