GeneBe

NR_131187.1:n.163-39606C>G

Variant names:

Variant summary

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

The NR_131187.1(LOC105376360):​n.163-39606C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,052 control chromosomes in the GnomAD database, including 3,229 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 0.19 ( 3229 hom., cov: 32)

Consequence

LOC105376360
NR_131187.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0250

Publications

1 publications found
Variant links:
Genes affected

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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105376360NR_131187.1 linkn.163-39606C>G intron_variant Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.193
AC:
29378
AN:
151934
Hom.:
3229
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0876
Gnomad AMI
AF:
0.148
Gnomad AMR
AF:
0.194
Gnomad ASJ
AF:
0.142
Gnomad EAS
AF:
0.173
Gnomad SAS
AF:
0.196
Gnomad FIN
AF:
0.277
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.249
Gnomad OTH
AF:
0.195
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29376
AN:
152052
Hom.:
3229
Cov.:
32
AF XY:
0.195
AC XY:
14480
AN XY:
74318
show subpopulations
African (AFR)
AF:
0.0874
AC:
3623
AN:
41464
American (AMR)
AF:
0.194
AC:
2957
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.142
AC:
492
AN:
3468
East Asian (EAS)
AF:
0.174
AC:
900
AN:
5184
South Asian (SAS)
AF:
0.195
AC:
941
AN:
4824
European-Finnish (FIN)
AF:
0.277
AC:
2927
AN:
10562
Middle Eastern (MID)
AF:
0.228
AC:
67
AN:
294
European-Non Finnish (NFE)
AF:
0.249
AC:
16920
AN:
67964
Other (OTH)
AF:
0.196
AC:
414
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1183
2366
3550
4733
5916
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
322
644
966
1288
1610
<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:
0.228
Hom.:
569
Bravo
AF:
0.182
Asia WGS
AF:
0.201
AC:
700
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.6
DANN
Benign
0.28
PhyloP100
-0.025

Splicing

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

Publications

Other links and lift over

dbSNP: rs10508262; hg19: chr10-3751274; API