ENST00000429211.2:n.126C>T

Variant summary

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

The ENST00000429211.2(ENSG00000226814):​n.126C>T 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 0.559 in 206,522 control chromosomes in the GnomAD database, including 32,369 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 0.56 ( 23688 hom., cov: 30)
Exomes 𝑓: 0.57 ( 8681 hom. )

Consequence

ENSG00000226814
ENST00000429211.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.45

Publications

8 publications found
Variant links:
Genes affected
ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

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=-0.61).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC100130137 n.192800696C>T intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000226814ENST00000429211.2 linkn.126C>T non_coding_transcript_exon_variant Exon 1 of 1 6
ENSG00000285280ENST00000644058.2 linkn.202-34502G>A intron_variant Intron 1 of 5
ENSG00000285280ENST00000644134.1 linkn.105-34502G>A intron_variant Intron 1 of 6

Frequencies

GnomAD3 genomes
AF:
0.556
AC:
84303
AN:
151642
Hom.:
23662
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.620
Gnomad AMI
AF:
0.678
Gnomad AMR
AF:
0.529
Gnomad ASJ
AF:
0.607
Gnomad EAS
AF:
0.630
Gnomad SAS
AF:
0.607
Gnomad FIN
AF:
0.413
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.532
Gnomad OTH
AF:
0.553
GnomAD4 exome
AF:
0.568
AC:
31098
AN:
54762
Hom.:
8681
Cov.:
0
AF XY:
0.571
AC XY:
18458
AN XY:
32344
show subpopulations
African (AFR)
AF:
0.644
AC:
1084
AN:
1682
American (AMR)
AF:
0.506
AC:
3378
AN:
6676
Ashkenazi Jewish (ASJ)
AF:
0.636
AC:
476
AN:
748
East Asian (EAS)
AF:
0.657
AC:
2356
AN:
3586
South Asian (SAS)
AF:
0.627
AC:
4009
AN:
6398
European-Finnish (FIN)
AF:
0.478
AC:
2626
AN:
5496
Middle Eastern (MID)
AF:
0.655
AC:
1051
AN:
1604
European-Non Finnish (NFE)
AF:
0.565
AC:
14952
AN:
26442
Other (OTH)
AF:
0.547
AC:
1166
AN:
2130
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.558
Heterozygous variant carriers
0
589
1178
1768
2357
2946
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
296
592
888
1184
1480
<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:
0.556
AC:
84375
AN:
151760
Hom.:
23688
Cov.:
30
AF XY:
0.553
AC XY:
40979
AN XY:
74132
show subpopulations
African (AFR)
AF:
0.620
AC:
25649
AN:
41386
American (AMR)
AF:
0.528
AC:
8051
AN:
15236
Ashkenazi Jewish (ASJ)
AF:
0.607
AC:
2106
AN:
3470
East Asian (EAS)
AF:
0.630
AC:
3258
AN:
5170
South Asian (SAS)
AF:
0.606
AC:
2910
AN:
4802
European-Finnish (FIN)
AF:
0.413
AC:
4337
AN:
10494
Middle Eastern (MID)
AF:
0.603
AC:
176
AN:
292
European-Non Finnish (NFE)
AF:
0.532
AC:
36107
AN:
67900
Other (OTH)
AF:
0.554
AC:
1163
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1870
3740
5610
7480
9350
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
728
1456
2184
2912
3640
<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:
0.549
Hom.:
3443
Bravo
AF:
0.563
Asia WGS
AF:
0.644
AC:
2236
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
1.9
DANN
Benign
0.61
PhyloP100
2.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs2179652; hg19: chr1-192769826; API