6-22694600-G-T

Variant summary

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

The NR_134613.1(LINC03005):​n.204+23121C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,174 control chromosomes in the GnomAD database, including 53,389 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 0.83 ( 53389 hom., cov: 33)

Consequence

LINC03005
NR_134613.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.465
Variant links:
Genes affected
LINC03005 (HGNC:56130): (long intergenic non-protein coding RNA 3005)

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC03005NR_134613.1 linkn.204+23121C>A intron_variant Intron 1 of 1
LINC03005NR_134614.1 linkn.204+23121C>A intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.835
AC:
126891
AN:
152056
Hom.:
53331
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.921
Gnomad AMI
AF:
0.950
Gnomad AMR
AF:
0.867
Gnomad ASJ
AF:
0.780
Gnomad EAS
AF:
0.653
Gnomad SAS
AF:
0.800
Gnomad FIN
AF:
0.825
Gnomad MID
AF:
0.896
Gnomad NFE
AF:
0.794
Gnomad OTH
AF:
0.820
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.835
AC:
127010
AN:
152174
Hom.:
53389
Cov.:
33
AF XY:
0.835
AC XY:
62132
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.921
Gnomad4 AMR
AF:
0.867
Gnomad4 ASJ
AF:
0.780
Gnomad4 EAS
AF:
0.652
Gnomad4 SAS
AF:
0.799
Gnomad4 FIN
AF:
0.825
Gnomad4 NFE
AF:
0.794
Gnomad4 OTH
AF:
0.819
Alfa
AF:
0.805
Hom.:
60595
Bravo
AF:
0.844
Asia WGS
AF:
0.732
AC:
2544
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.45
DANN
Benign
0.43

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: rs1555108; hg19: chr6-22694829; API