chr16-9581389-T-G

Variant summary

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

The ENST00000634367.3(LINC02177):​n.622+14799T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,144 control chromosomes in the GnomAD database, including 2,456 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 0.17 ( 2456 hom., cov: 31)

Consequence

LINC02177
ENST00000634367.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.589

Publications

6 publications found
Variant links:
Genes affected
LINC02177 (HGNC:53039): (long intergenic non-protein coding RNA 2177)

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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02177ENST00000634367.3 linkn.622+14799T>G intron_variant Intron 4 of 4 5
LINC02177ENST00000784503.1 linkn.652+14799T>G intron_variant Intron 4 of 4
LINC02177ENST00000784504.1 linkn.480+14799T>G intron_variant Intron 4 of 4

Frequencies

GnomAD3 genomes
AF:
0.166
AC:
25305
AN:
152026
Hom.:
2458
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.181
Gnomad AMI
AF:
0.0263
Gnomad AMR
AF:
0.141
Gnomad ASJ
AF:
0.0887
Gnomad EAS
AF:
0.502
Gnomad SAS
AF:
0.129
Gnomad FIN
AF:
0.162
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.148
Gnomad OTH
AF:
0.153
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.166
AC:
25326
AN:
152144
Hom.:
2456
Cov.:
31
AF XY:
0.166
AC XY:
12331
AN XY:
74372
show subpopulations
African (AFR)
AF:
0.181
AC:
7491
AN:
41484
American (AMR)
AF:
0.142
AC:
2164
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.0887
AC:
308
AN:
3472
East Asian (EAS)
AF:
0.502
AC:
2593
AN:
5168
South Asian (SAS)
AF:
0.128
AC:
617
AN:
4818
European-Finnish (FIN)
AF:
0.162
AC:
1716
AN:
10590
Middle Eastern (MID)
AF:
0.0782
AC:
23
AN:
294
European-Non Finnish (NFE)
AF:
0.148
AC:
10065
AN:
68006
Other (OTH)
AF:
0.154
AC:
325
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1032
2064
3097
4129
5161
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
276
552
828
1104
1380
<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:
0.160
Hom.:
9232
Bravo
AF:
0.172
Asia WGS
AF:
0.325
AC:
1130
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
7.5
DANN
Benign
0.71
PhyloP100
0.59

Splicing

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

Publications

Other links and lift over

dbSNP: rs12325410; hg19: chr16-9675246; API