rs17042171

Variant summary

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

The ENST00000754041.1(LINC01438):​n.215+3408C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,068 control chromosomes in the GnomAD database, including 3,465 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 0.19 ( 3465 hom., cov: 32)

Consequence

LINC01438
ENST00000754041.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

44 publications found
Variant links:
Genes affected
LINC01438 (HGNC:50757): (long intergenic non-protein coding RNA 1438)

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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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
LINC01438ENST00000754041.1 linkn.215+3408C>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.192
AC:
29240
AN:
151950
Hom.:
3456
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.247
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.232
Gnomad ASJ
AF:
0.305
Gnomad EAS
AF:
0.502
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.153
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.189
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29281
AN:
152068
Hom.:
3465
Cov.:
32
AF XY:
0.200
AC XY:
14849
AN XY:
74324
show subpopulations
African (AFR)
AF:
0.247
AC:
10259
AN:
41480
American (AMR)
AF:
0.233
AC:
3551
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.305
AC:
1057
AN:
3468
East Asian (EAS)
AF:
0.503
AC:
2601
AN:
5168
South Asian (SAS)
AF:
0.134
AC:
646
AN:
4826
European-Finnish (FIN)
AF:
0.153
AC:
1615
AN:
10558
Middle Eastern (MID)
AF:
0.221
AC:
65
AN:
294
European-Non Finnish (NFE)
AF:
0.133
AC:
9071
AN:
67978
Other (OTH)
AF:
0.191
AC:
403
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1169
2338
3506
4675
5844
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
304
608
912
1216
1520
<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:
0.151
Hom.:
6679
Bravo
AF:
0.202
Asia WGS
AF:
0.262
AC:
911
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
6.1
DANN
Benign
0.40
PhyloP100
-0.0070

Splicing

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

Publications

Other links and lift over

dbSNP: rs17042171; hg19: chr4-111708287; API