GeneBe

NR_125390.1:n.471+154130C>T

Variant names:

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+154130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,120 control chromosomes in the GnomAD database, including 4,247 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 0.17 ( 4247 hom., cov: 32)

Consequence

LOC101927066
NR_125390.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.187

Publications

0 publications found
Variant links:
Genes affected

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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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC101927066NR_125390.1 linkn.471+154130C>T intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
26360
AN:
152002
Hom.:
4245
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.428
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.126
Gnomad ASJ
AF:
0.0652
Gnomad EAS
AF:
0.0886
Gnomad SAS
AF:
0.132
Gnomad FIN
AF:
0.0526
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0671
Gnomad OTH
AF:
0.127
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.173
AC:
26386
AN:
152120
Hom.:
4247
Cov.:
32
AF XY:
0.169
AC XY:
12594
AN XY:
74362
show subpopulations
African (AFR)
AF:
0.428
AC:
17736
AN:
41438
American (AMR)
AF:
0.126
AC:
1927
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.0652
AC:
226
AN:
3468
East Asian (EAS)
AF:
0.0878
AC:
454
AN:
5168
South Asian (SAS)
AF:
0.131
AC:
632
AN:
4824
European-Finnish (FIN)
AF:
0.0526
AC:
558
AN:
10606
Middle Eastern (MID)
AF:
0.0918
AC:
27
AN:
294
European-Non Finnish (NFE)
AF:
0.0671
AC:
4562
AN:
68004
Other (OTH)
AF:
0.124
AC:
263
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
910
1821
2731
3642
4552
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
254
508
762
1016
1270
<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:
0.116
Hom.:
433
Bravo
AF:
0.190
Asia WGS
AF:
0.115
AC:
400
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.8
DANN
Benign
0.64
PhyloP100
-0.19

Splicing

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

Publications

Other links and lift over

dbSNP: rs2439700; hg19: chr8-98277168; API