ENST00000554732.5:n.222-2614C>T

Variant summary

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

The ENST00000554732.5(LINC00639):​n.222-2614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,102 control chromosomes in the GnomAD database, including 1,917 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 0.14 ( 1917 hom., cov: 32)

Consequence

LINC00639
ENST00000554732.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193

Publications

4 publications found
Variant links:
Genes affected
LINC00639 (HGNC:27502): (long intergenic non-protein coding RNA 639)

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 (AMR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00639NR_039982.1 linkn.160-2614C>T intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00639ENST00000554732.5 linkn.222-2614C>T intron_variant Intron 3 of 5 1
LINC00639ENST00000553932.5 linkn.155-2614C>T intron_variant Intron 2 of 6 2
LINC00639ENST00000556116.2 linkn.246-2614C>T intron_variant Intron 2 of 7 4

Frequencies

GnomAD3 genomes
AF:
0.145
AC:
21972
AN:
151984
Hom.:
1913
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.143
Gnomad AMI
AF:
0.203
Gnomad AMR
AF:
0.300
Gnomad ASJ
AF:
0.153
Gnomad EAS
AF:
0.102
Gnomad SAS
AF:
0.160
Gnomad FIN
AF:
0.139
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.112
Gnomad OTH
AF:
0.174
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.145
AC:
22007
AN:
152102
Hom.:
1917
Cov.:
32
AF XY:
0.150
AC XY:
11175
AN XY:
74356
show subpopulations
African (AFR)
AF:
0.143
AC:
5925
AN:
41488
American (AMR)
AF:
0.300
AC:
4589
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.153
AC:
531
AN:
3468
East Asian (EAS)
AF:
0.102
AC:
528
AN:
5172
South Asian (SAS)
AF:
0.162
AC:
782
AN:
4830
European-Finnish (FIN)
AF:
0.139
AC:
1465
AN:
10550
Middle Eastern (MID)
AF:
0.122
AC:
36
AN:
294
European-Non Finnish (NFE)
AF:
0.112
AC:
7597
AN:
67988
Other (OTH)
AF:
0.175
AC:
369
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
947
1894
2840
3787
4734
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
232
464
696
928
1160
<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:
0.129
Hom.:
2308
Bravo
AF:
0.161
Asia WGS
AF:
0.142
AC:
495
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
0.66
DANN
Benign
0.28
PhyloP100
-0.19

Splicing

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

Publications

Other links and lift over

dbSNP: rs17108400; hg19: chr14-39311022; API