GeneBe

rs34122827

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000439454.3(LINC00376):​n.459-10117_459-10114delAAGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 12344 hom., cov: 0)

Consequence

LINC00376
ENST00000439454.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.531

Publications

4 publications found
Variant links:
Genes affected
LINC00376 (HGNC:42701): (long intergenic non-protein coding RNA 376)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00376NR_126409.1 linkn.424-10117_424-10114delAAGT intron_variant Intron 5 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00376ENST00000439454.3 linkn.459-10117_459-10114delAAGT intron_variant Intron 5 of 6 5
LINC00376ENST00000836363.1 linkn.340-10117_340-10114delAAGT intron_variant Intron 4 of 5
LINC00376ENST00000836364.1 linkn.350-10117_350-10114delAAGT intron_variant Intron 4 of 5

Frequencies

GnomAD3 genomes
AF:
0.391
AC:
59244
AN:
151622
Hom.:
12347
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.304
Gnomad AMI
AF:
0.502
Gnomad AMR
AF:
0.360
Gnomad ASJ
AF:
0.455
Gnomad EAS
AF:
0.0264
Gnomad SAS
AF:
0.387
Gnomad FIN
AF:
0.345
Gnomad MID
AF:
0.429
Gnomad NFE
AF:
0.480
Gnomad OTH
AF:
0.392
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.390
AC:
59246
AN:
151740
Hom.:
12344
Cov.:
0
AF XY:
0.381
AC XY:
28274
AN XY:
74138
show subpopulations
African (AFR)
AF:
0.304
AC:
12575
AN:
41390
American (AMR)
AF:
0.360
AC:
5486
AN:
15246
Ashkenazi Jewish (ASJ)
AF:
0.455
AC:
1577
AN:
3468
East Asian (EAS)
AF:
0.0264
AC:
137
AN:
5180
South Asian (SAS)
AF:
0.387
AC:
1863
AN:
4816
European-Finnish (FIN)
AF:
0.345
AC:
3626
AN:
10522
Middle Eastern (MID)
AF:
0.441
AC:
127
AN:
288
European-Non Finnish (NFE)
AF:
0.480
AC:
32588
AN:
67822
Other (OTH)
AF:
0.386
AC:
811
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
1731
3462
5194
6925
8656
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
550
1100
1650
2200
2750
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.436
Hom.:
1827
Bravo
AF:
0.385
Asia WGS
AF:
0.208
AC:
725
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs34122827; hg19: chr13-63778777; API