rs2142450

Variant summary

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

The NM_003489.4(NRIP1):​c.*1635G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,148 control chromosomes in the GnomAD database, including 2,334 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 0.16 ( 2330 hom., cov: 32)
Exomes 𝑓: 0.22 ( 4 hom. )

Consequence

NRIP1
NM_003489.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.105

Publications

8 publications found
Variant links:
Genes affected
NRIP1 (HGNC:8001): (nuclear receptor interacting protein 1) Nuclear receptor interacting protein 1 (NRIP1) is a nuclear protein that specifically interacts with the hormone-dependent activation domain AF2 of nuclear receptors. Also known as RIP140, this protein modulates transcriptional activity of the estrogen receptor. [provided by RefSeq, Jul 2008]
ASMER1 (HGNC:53135): (adipocyte associated metabolic related lncRNA 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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NRIP1NM_003489.4 linkc.*1635G>A 3_prime_UTR_variant Exon 4 of 4 ENST00000318948.7 NP_003480.2 P48552A8K171

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NRIP1ENST00000318948.7 linkc.*1635G>A 3_prime_UTR_variant Exon 4 of 4 2 NM_003489.4 ENSP00000327213.4 P48552

Frequencies

GnomAD3 genomes
AF:
0.164
AC:
24924
AN:
151886
Hom.:
2330
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0952
Gnomad AMI
AF:
0.298
Gnomad AMR
AF:
0.129
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.140
Gnomad SAS
AF:
0.150
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.208
Gnomad OTH
AF:
0.176
GnomAD4 exome
AF:
0.215
AC:
31
AN:
144
Hom.:
4
Cov.:
0
AF XY:
0.195
AC XY:
16
AN XY:
82
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)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.207
AC:
29
AN:
140
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
1.00
AC:
2
AN:
2
Other (OTH)
AF:
0.00
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.164
AC:
24940
AN:
152004
Hom.:
2330
Cov.:
32
AF XY:
0.162
AC XY:
12015
AN XY:
74322
show subpopulations
African (AFR)
AF:
0.0953
AC:
3956
AN:
41516
American (AMR)
AF:
0.129
AC:
1971
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.154
AC:
535
AN:
3470
East Asian (EAS)
AF:
0.140
AC:
726
AN:
5184
South Asian (SAS)
AF:
0.151
AC:
725
AN:
4814
European-Finnish (FIN)
AF:
0.207
AC:
2186
AN:
10574
Middle Eastern (MID)
AF:
0.255
AC:
75
AN:
294
European-Non Finnish (NFE)
AF:
0.208
AC:
14125
AN:
67870
Other (OTH)
AF:
0.175
AC:
369
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1053
2105
3158
4210
5263
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
278
556
834
1112
1390
<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:
0.197
Hom.:
3138
Bravo
AF:
0.156
Asia WGS
AF:
0.148
AC:
515
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.80
DANN
Benign
0.70
PhyloP100
-0.10
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs2142450; hg19: chr21-16335402; API