rs906310

Variant summary

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

The ENST00000503768.6(LINC00923):​n.599-2639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,048 control chromosomes in the GnomAD database, including 15,788 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 0.45 ( 15788 hom., cov: 33)

Consequence

LINC00923
ENST00000503768.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.506
Variant links:
Genes affected
LINC00923 (HGNC:28088): (long intergenic non-protein coding RNA 923)

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=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00923NR_024172.1 linkn.478-2639C>T intron_variant Intron 1 of 2
LINC00923NR_024173.1 linkn.478-17817C>T intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00923ENST00000503768.6 linkn.599-2639C>T intron_variant Intron 1 of 2 1
LINC00923ENST00000503874.3 linkn.599-17817C>T intron_variant Intron 1 of 1 1
LINC00923ENST00000614972.4 linkn.689-17817C>T intron_variant Intron 2 of 5 5

Frequencies

GnomAD3 genomes
AF:
0.450
AC:
68342
AN:
151928
Hom.:
15793
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.416
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.402
Gnomad ASJ
AF:
0.576
Gnomad EAS
AF:
0.745
Gnomad SAS
AF:
0.560
Gnomad FIN
AF:
0.494
Gnomad MID
AF:
0.510
Gnomad NFE
AF:
0.437
Gnomad OTH
AF:
0.447
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.450
AC:
68352
AN:
152048
Hom.:
15788
Cov.:
33
AF XY:
0.456
AC XY:
33922
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.415
Gnomad4 AMR
AF:
0.402
Gnomad4 ASJ
AF:
0.576
Gnomad4 EAS
AF:
0.744
Gnomad4 SAS
AF:
0.559
Gnomad4 FIN
AF:
0.494
Gnomad4 NFE
AF:
0.437
Gnomad4 OTH
AF:
0.447
Alfa
AF:
0.419
Hom.:
12844
Bravo
AF:
0.436
Asia WGS
AF:
0.626
AC:
2176
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
6.0
DANN
Benign
0.87

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: rs906310; hg19: chr15-98304530; API