rs1463666

Variant summary

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

The NR_126452.2(LINC00508):​n.312-13722T>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 0.236 in 151,924 control chromosomes in the GnomAD database, including 6,725 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 0.24 ( 6725 hom., cov: 32)

Consequence

LINC00508
NR_126452.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.502
Variant links:
Genes affected

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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC00508NR_126452.2 linkuse as main transcriptn.312-13722T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.236
AC:
35753
AN:
151806
Hom.:
6722
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.509
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.148
Gnomad ASJ
AF:
0.0573
Gnomad EAS
AF:
0.495
Gnomad SAS
AF:
0.0916
Gnomad FIN
AF:
0.140
Gnomad MID
AF:
0.153
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.208
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.236
AC:
35789
AN:
151924
Hom.:
6725
Cov.:
32
AF XY:
0.234
AC XY:
17356
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.509
Gnomad4 AMR
AF:
0.147
Gnomad4 ASJ
AF:
0.0573
Gnomad4 EAS
AF:
0.494
Gnomad4 SAS
AF:
0.0904
Gnomad4 FIN
AF:
0.140
Gnomad4 NFE
AF:
0.107
Gnomad4 OTH
AF:
0.205
Alfa
AF:
0.178
Hom.:
652
Bravo
AF:
0.252
Asia WGS
AF:
0.298
AC:
1035
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.6
DANN
Benign
0.14

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: rs1463666; hg19: chr12-128383372; API