rs1400363

Variant summary

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

The ENST00000656681.1(LINC02428):​n.469+73271A>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 0.491 in 151,866 control chromosomes in the GnomAD database, including 19,277 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 0.49 ( 19277 hom., cov: 31)

Consequence

LINC02428
ENST00000656681.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.282
Variant links:
Genes affected
LINC02428 (HGNC:53359): (long intergenic non-protein coding RNA 2428)

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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
LINC02428ENST00000656681.1 linkuse as main transcriptn.469+73271A>C intron_variant, non_coding_transcript_variant
LINC02428ENST00000513793.5 linkuse as main transcriptn.136+73271A>C intron_variant, non_coding_transcript_variant 5
LINC02428ENST00000656104.1 linkuse as main transcriptn.470-13527A>C intron_variant, non_coding_transcript_variant
LINC02428ENST00000668077.1 linkuse as main transcriptn.243-13527A>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.491
AC:
74503
AN:
151748
Hom.:
19239
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.666
Gnomad AMI
AF:
0.327
Gnomad AMR
AF:
0.437
Gnomad ASJ
AF:
0.542
Gnomad EAS
AF:
0.379
Gnomad SAS
AF:
0.439
Gnomad FIN
AF:
0.425
Gnomad MID
AF:
0.478
Gnomad NFE
AF:
0.419
Gnomad OTH
AF:
0.504
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.491
AC:
74585
AN:
151866
Hom.:
19277
Cov.:
31
AF XY:
0.489
AC XY:
36273
AN XY:
74192
show subpopulations
Gnomad4 AFR
AF:
0.666
Gnomad4 AMR
AF:
0.437
Gnomad4 ASJ
AF:
0.542
Gnomad4 EAS
AF:
0.379
Gnomad4 SAS
AF:
0.438
Gnomad4 FIN
AF:
0.425
Gnomad4 NFE
AF:
0.419
Gnomad4 OTH
AF:
0.500
Alfa
AF:
0.443
Hom.:
7173
Bravo
AF:
0.500
Asia WGS
AF:
0.425
AC:
1480
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.5
DANN
Benign
0.64

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: rs1400363; hg19: chr4-104250722; API