1-60629886-G-C

Variant summary

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

The ENST00000661045.1(LINC01748):​n.104+10125C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,688 control chromosomes in the GnomAD database, including 16,881 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 0.47 ( 16881 hom., cov: 31)

Consequence

LINC01748
ENST00000661045.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.194
Variant links:
Genes affected
LINC01748 (HGNC:52535): (long intergenic non-protein coding RNA 1748)

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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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
LINC01748ENST00000439156.2 linkn.336+10125C>G intron_variant Intron 2 of 7 5
LINC01748ENST00000661045.1 linkn.104+10125C>G intron_variant Intron 1 of 3
LINC01748ENST00000662065.1 linkn.343+10125C>G intron_variant Intron 2 of 6

Frequencies

GnomAD3 genomes
AF:
0.470
AC:
71196
AN:
151572
Hom.:
16867
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.462
Gnomad AMI
AF:
0.454
Gnomad AMR
AF:
0.504
Gnomad ASJ
AF:
0.479
Gnomad EAS
AF:
0.636
Gnomad SAS
AF:
0.581
Gnomad FIN
AF:
0.411
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.454
Gnomad OTH
AF:
0.488
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.470
AC:
71230
AN:
151688
Hom.:
16881
Cov.:
31
AF XY:
0.471
AC XY:
34921
AN XY:
74134
show subpopulations
African (AFR)
AF:
0.461
AC:
19092
AN:
41370
American (AMR)
AF:
0.504
AC:
7697
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.479
AC:
1661
AN:
3470
East Asian (EAS)
AF:
0.636
AC:
3285
AN:
5168
South Asian (SAS)
AF:
0.581
AC:
2799
AN:
4814
European-Finnish (FIN)
AF:
0.411
AC:
4296
AN:
10448
Middle Eastern (MID)
AF:
0.500
AC:
146
AN:
292
European-Non Finnish (NFE)
AF:
0.454
AC:
30800
AN:
67846
Other (OTH)
AF:
0.494
AC:
1041
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1880
3761
5641
7522
9402
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
666
1332
1998
2664
3330
<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:
0.283
Hom.:
632
Bravo
AF:
0.475
Asia WGS
AF:
0.590
AC:
2044
AN:
3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.9
DANN
Benign
0.60
PhyloP100
-0.19
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs472913; hg19: chr1-61095558; API