chr5-106843207-C-T

Variant summary

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

The ENST00000505997.2(LINC01950):​n.260+854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,816 control chromosomes in the GnomAD database, including 4,603 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 ( 4603 hom., cov: 31)

Consequence

LINC01950
ENST00000505997.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720

Publications

3 publications found
Variant links:
Genes affected
LINC01950 (HGNC:52773): (long intergenic non-protein coding RNA 1950)

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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC01950NR_104671.1 linkn.144-24730G>A intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01950ENST00000505997.2 linkn.260+854G>A intron_variant Intron 2 of 2 3
LINC01950ENST00000513273.1 linkn.144-24730G>A intron_variant Intron 2 of 3 2
LINC01950ENST00000657922.2 linkn.201-24730G>A intron_variant Intron 2 of 3
LINC01950ENST00000661979.1 linkn.114-24730G>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.235
AC:
35588
AN:
151698
Hom.:
4601
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.111
Gnomad AMI
AF:
0.346
Gnomad AMR
AF:
0.260
Gnomad ASJ
AF:
0.316
Gnomad EAS
AF:
0.359
Gnomad SAS
AF:
0.283
Gnomad FIN
AF:
0.246
Gnomad MID
AF:
0.261
Gnomad NFE
AF:
0.283
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.235
AC:
35606
AN:
151816
Hom.:
4603
Cov.:
31
AF XY:
0.236
AC XY:
17526
AN XY:
74166
show subpopulations
African (AFR)
AF:
0.111
AC:
4599
AN:
41432
American (AMR)
AF:
0.260
AC:
3967
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
0.316
AC:
1095
AN:
3466
East Asian (EAS)
AF:
0.359
AC:
1838
AN:
5124
South Asian (SAS)
AF:
0.283
AC:
1362
AN:
4810
European-Finnish (FIN)
AF:
0.246
AC:
2590
AN:
10516
Middle Eastern (MID)
AF:
0.252
AC:
73
AN:
290
European-Non Finnish (NFE)
AF:
0.283
AC:
19226
AN:
67912
Other (OTH)
AF:
0.257
AC:
540
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1334
2669
4003
5338
6672
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
382
764
1146
1528
1910
<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:
0.267
Hom.:
1916
Bravo
AF:
0.228
Asia WGS
AF:
0.310
AC:
1078
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.8
DANN
Benign
0.47
PhyloP100
-0.072

Splicing

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

Publications

Other links and lift over

dbSNP: rs17159152; hg19: chr5-106178908; API