rs288423

Variant summary

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

The ENST00000615399.1(LINC00923):​n.411+26641C>T 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 0.497 in 152,004 control chromosomes in the GnomAD database, including 19,284 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 0.50 ( 19284 hom., cov: 33)

Consequence

LINC00923
ENST00000615399.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.143
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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
LINC00923ENST00000615399.1 linkuse as main transcriptn.411+26641C>T intron_variant, non_coding_transcript_variant 5
LINC00923ENST00000658023.1 linkuse as main transcriptn.357+26641C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.496
AC:
75396
AN:
151886
Hom.:
19254
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.587
Gnomad AMI
AF:
0.384
Gnomad AMR
AF:
0.547
Gnomad ASJ
AF:
0.336
Gnomad EAS
AF:
0.545
Gnomad SAS
AF:
0.508
Gnomad FIN
AF:
0.552
Gnomad MID
AF:
0.364
Gnomad NFE
AF:
0.428
Gnomad OTH
AF:
0.473
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.497
AC:
75479
AN:
152004
Hom.:
19284
Cov.:
33
AF XY:
0.502
AC XY:
37325
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.587
Gnomad4 AMR
AF:
0.548
Gnomad4 ASJ
AF:
0.336
Gnomad4 EAS
AF:
0.545
Gnomad4 SAS
AF:
0.506
Gnomad4 FIN
AF:
0.552
Gnomad4 NFE
AF:
0.428
Gnomad4 OTH
AF:
0.478
Alfa
AF:
0.480
Hom.:
2198
Bravo
AF:
0.499
Asia WGS
AF:
0.546
AC:
1899
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.21
DANN
Benign
0.57

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: rs288423; hg19: chr15-98168641; API