chr5-25173090-T-C

Variant summary

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

The ENST00000507600.3(LINC02228):​n.261-5899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,096 control chromosomes in the GnomAD database, including 2,060 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 0.16 ( 2060 hom., cov: 32)

Consequence

LINC02228
ENST00000507600.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.726

Publications

2 publications found
Variant links:
Genes affected
LINC02228 (HGNC:53097): (long intergenic non-protein coding RNA 2228)
LINC02211 (HGNC:53078): (long intergenic non-protein coding RNA 2211)

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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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC02228NR_147006.1 linkn.211-5899A>G intron_variant Intron 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02228ENST00000507600.3 linkn.261-5899A>G intron_variant Intron 1 of 4 2
LINC02228ENST00000641261.2 linkn.511-5899A>G intron_variant Intron 1 of 4
LINC02228ENST00000641970.2 linkn.263-5899A>G intron_variant Intron 1 of 5

Frequencies

GnomAD3 genomes
AF:
0.162
AC:
24594
AN:
151978
Hom.:
2054
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.226
Gnomad AMI
AF:
0.264
Gnomad AMR
AF:
0.108
Gnomad ASJ
AF:
0.135
Gnomad EAS
AF:
0.0345
Gnomad SAS
AF:
0.137
Gnomad FIN
AF:
0.156
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.147
Gnomad OTH
AF:
0.164
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.162
AC:
24632
AN:
152096
Hom.:
2060
Cov.:
32
AF XY:
0.158
AC XY:
11783
AN XY:
74352
show subpopulations
African (AFR)
AF:
0.226
AC:
9398
AN:
41494
American (AMR)
AF:
0.108
AC:
1647
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.135
AC:
469
AN:
3466
East Asian (EAS)
AF:
0.0344
AC:
178
AN:
5174
South Asian (SAS)
AF:
0.138
AC:
667
AN:
4820
European-Finnish (FIN)
AF:
0.156
AC:
1648
AN:
10578
Middle Eastern (MID)
AF:
0.0918
AC:
27
AN:
294
European-Non Finnish (NFE)
AF:
0.147
AC:
10007
AN:
67976
Other (OTH)
AF:
0.166
AC:
350
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1080
2160
3241
4321
5401
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
258
516
774
1032
1290
<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:
0.167
Hom.:
268
Bravo
AF:
0.159
Asia WGS
AF:
0.128
AC:
445
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.82
DANN
Benign
0.71
PhyloP100
-0.73

Splicing

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

Publications

Other links and lift over

dbSNP: rs2014790; hg19: chr5-25173199; API