rs6921233

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+5854G>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 0.491 in 152,008 control chromosomes in the GnomAD database, including 18,384 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 ( 18384 hom., cov: 32)

Consequence

LINC03004
ENST00000635999.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.602
Variant links:
Genes affected
LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 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
LINC03004ENST00000635999.1 linkuse as main transcriptn.433+5854G>A intron_variant, non_coding_transcript_variant 5
LINC03004ENST00000638039.1 linkuse as main transcriptn.438+5854G>A intron_variant, non_coding_transcript_variant 5
LINC03004ENST00000646621.1 linkuse as main transcriptn.414+5854G>A intron_variant, non_coding_transcript_variant
LINC03004ENST00000666119.1 linkuse as main transcriptn.392+5854G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.491
AC:
74588
AN:
151890
Hom.:
18382
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.535
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.453
Gnomad ASJ
AF:
0.392
Gnomad EAS
AF:
0.535
Gnomad SAS
AF:
0.449
Gnomad FIN
AF:
0.547
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.471
Gnomad OTH
AF:
0.503
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.491
AC:
74609
AN:
152008
Hom.:
18384
Cov.:
32
AF XY:
0.494
AC XY:
36676
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.535
Gnomad4 AMR
AF:
0.452
Gnomad4 ASJ
AF:
0.392
Gnomad4 EAS
AF:
0.536
Gnomad4 SAS
AF:
0.447
Gnomad4 FIN
AF:
0.547
Gnomad4 NFE
AF:
0.471
Gnomad4 OTH
AF:
0.498
Alfa
AF:
0.470
Hom.:
16374
Bravo
AF:
0.485
Asia WGS
AF:
0.484
AC:
1686
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
6.7
DANN
Benign
0.55

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: rs6921233; hg19: chr6-138001115; API