chr5-118158945-G-A

Variant summary

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

The NR_104997.1(LINC02147):​n.171-106409G>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 0.596 in 151,880 control chromosomes in the GnomAD database, including 30,369 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 0.60 ( 30369 hom., cov: 31)

Consequence

LINC02147
NR_104997.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276
Variant links:
Genes affected
LINC02147 (HGNC:53007): (long intergenic non-protein coding RNA 2147)
LINC02208 (HGNC:52978): (long intergenic non-protein coding RNA 2208)

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=-0.66).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02147NR_104997.1 linkuse as main transcriptn.171-106409G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC02147ENST00000509367.2 linkuse as main transcriptn.277-28520G>A intron_variant, non_coding_transcript_variant 2
LINC02208ENST00000660173.1 linkuse as main transcriptn.688-7484C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.595
AC:
90343
AN:
151762
Hom.:
30313
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.889
Gnomad AMI
AF:
0.603
Gnomad AMR
AF:
0.451
Gnomad ASJ
AF:
0.541
Gnomad EAS
AF:
0.0218
Gnomad SAS
AF:
0.401
Gnomad FIN
AF:
0.416
Gnomad MID
AF:
0.699
Gnomad NFE
AF:
0.536
Gnomad OTH
AF:
0.597
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.596
AC:
90449
AN:
151880
Hom.:
30369
Cov.:
31
AF XY:
0.582
AC XY:
43143
AN XY:
74188
show subpopulations
Gnomad4 AFR
AF:
0.889
Gnomad4 AMR
AF:
0.450
Gnomad4 ASJ
AF:
0.541
Gnomad4 EAS
AF:
0.0216
Gnomad4 SAS
AF:
0.400
Gnomad4 FIN
AF:
0.416
Gnomad4 NFE
AF:
0.536
Gnomad4 OTH
AF:
0.596
Alfa
AF:
0.536
Hom.:
49860
Bravo
AF:
0.611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
8.2
DANN
Benign
0.62

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: rs10079352; hg19: chr5-117494640; API