GeneBe

chr2-8301605-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000430192.5(LINC00299):​n.90-1812G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,566 control chromosomes in the GnomAD database, including 4,625 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 0.23 ( 4625 hom., cov: 30)

Consequence

LINC00299
ENST00000430192.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Publications

13 publications found
Variant links:
Genes affected
LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00299NR_034135.1 linkn.330-1812G>C intron_variant Intron 2 of 8
LINC00299NR_152741.1 linkn.454-1812G>C intron_variant Intron 3 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00299ENST00000430192.5 linkn.90-1812G>C intron_variant Intron 1 of 7 1
LINC00299ENST00000442956.1 linkn.454-1812G>C intron_variant Intron 3 of 9 2
LINC00299ENST00000668369.1 linkn.*204G>C downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.234
AC:
35486
AN:
151448
Hom.:
4628
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.116
Gnomad AMI
AF:
0.284
Gnomad AMR
AF:
0.257
Gnomad ASJ
AF:
0.175
Gnomad EAS
AF:
0.272
Gnomad SAS
AF:
0.254
Gnomad FIN
AF:
0.351
Gnomad MID
AF:
0.178
Gnomad NFE
AF:
0.282
Gnomad OTH
AF:
0.226
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.234
AC:
35491
AN:
151566
Hom.:
4625
Cov.:
30
AF XY:
0.237
AC XY:
17521
AN XY:
74052
show subpopulations
African (AFR)
AF:
0.115
AC:
4773
AN:
41398
American (AMR)
AF:
0.258
AC:
3921
AN:
15216
Ashkenazi Jewish (ASJ)
AF:
0.175
AC:
605
AN:
3466
East Asian (EAS)
AF:
0.273
AC:
1395
AN:
5118
South Asian (SAS)
AF:
0.254
AC:
1221
AN:
4804
European-Finnish (FIN)
AF:
0.351
AC:
3660
AN:
10442
Middle Eastern (MID)
AF:
0.171
AC:
50
AN:
292
European-Non Finnish (NFE)
AF:
0.282
AC:
19133
AN:
67824
Other (OTH)
AF:
0.227
AC:
475
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1169
2338
3508
4677
5846
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
384
768
1152
1536
1920
<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:
0.148
Hom.:
284
Bravo
AF:
0.226
Asia WGS
AF:
0.277
AC:
964
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
0.54
DANN
Benign
0.41
PhyloP100
-1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs13416555; hg19: chr2-8441735; API