21-44990632-C-T

Variant summary

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

The ENST00000434081.1(LINC00163):​n.1387G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,230 control chromosomes in the GnomAD database, including 19,706 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 0.48 ( 19687 hom., cov: 34)
Exomes 𝑓: 0.65 ( 19 hom. )

Consequence

LINC00163
ENST00000434081.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28

Publications

3 publications found
Variant links:
Genes affected
LINC00163 (HGNC:33165): (long intergenic non-protein coding RNA 163)

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=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00163NR_033840.1 linkn.1387G>A non_coding_transcript_exon_variant Exon 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00163ENST00000434081.1 linkn.1387G>A non_coding_transcript_exon_variant Exon 2 of 2 1
LINC00163ENST00000439088.1 linkn.1367G>A non_coding_transcript_exon_variant Exon 2 of 2 1

Frequencies

GnomAD3 genomes
AF:
0.477
AC:
72518
AN:
152034
Hom.:
19692
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.546
Gnomad AMR
AF:
0.513
Gnomad ASJ
AF:
0.523
Gnomad EAS
AF:
0.661
Gnomad SAS
AF:
0.705
Gnomad FIN
AF:
0.609
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.580
Gnomad OTH
AF:
0.510
GnomAD4 exome
AF:
0.654
AC:
51
AN:
78
Hom.:
19
Cov.:
0
AF XY:
0.630
AC XY:
34
AN XY:
54
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.500
AC:
1
AN:
2
European-Finnish (FIN)
AF:
0.333
AC:
2
AN:
6
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.726
AC:
45
AN:
62
Other (OTH)
AF:
0.375
AC:
3
AN:
8
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.477
AC:
72534
AN:
152152
Hom.:
19687
Cov.:
34
AF XY:
0.482
AC XY:
35874
AN XY:
74358
show subpopulations
African (AFR)
AF:
0.202
AC:
8400
AN:
41496
American (AMR)
AF:
0.513
AC:
7849
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.523
AC:
1817
AN:
3472
East Asian (EAS)
AF:
0.660
AC:
3414
AN:
5172
South Asian (SAS)
AF:
0.707
AC:
3410
AN:
4826
European-Finnish (FIN)
AF:
0.609
AC:
6453
AN:
10596
Middle Eastern (MID)
AF:
0.578
AC:
170
AN:
294
European-Non Finnish (NFE)
AF:
0.580
AC:
39449
AN:
67980
Other (OTH)
AF:
0.509
AC:
1075
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1787
3574
5361
7148
8935
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
654
1308
1962
2616
3270
<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:
0.533
Hom.:
9366
Bravo
AF:
0.451
Asia WGS
AF:
0.645
AC:
2241
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
3.7
DANN
Benign
0.96
PhyloP100
-2.3

Splicing

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

Publications

Other links and lift over

dbSNP: rs11088977; hg19: chr21-46410547; API