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rs8066154

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020772.3(NUFIP2):c.2003-8538G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 143,826 control chromosomes in the GnomAD database, including 1,425 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 0.13 ( 1425 hom., cov: 30)

Consequence

NUFIP2
NM_020772.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08
Variant links:
Genes affected
NUFIP2 (HGNC:17634): (nuclear FMR1 interacting protein 2) Enables RNA binding activity. Located in cytoplasmic stress granule; cytosol; and nuclear body. Part of polysomal ribosome. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NUFIP2NM_020772.3 linkuse as main transcriptc.2003-8538G>A intron_variant ENST00000225388.9
NUFIP2XM_017024896.3 linkuse as main transcriptc.1526-8538G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NUFIP2ENST00000225388.9 linkuse as main transcriptc.2003-8538G>A intron_variant 1 NM_020772.3 P1Q7Z417-1
NUFIP2ENST00000579665.1 linkuse as main transcriptc.278-8538G>A intron_variant 1 Q7Z417-2

Frequencies

GnomAD3 genomes
AF:
0.133
AC:
19068
AN:
143712
Hom.:
1423
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.170
Gnomad AMI
AF:
0.195
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.107
Gnomad EAS
AF:
0.303
Gnomad SAS
AF:
0.194
Gnomad FIN
AF:
0.121
Gnomad MID
AF:
0.0473
Gnomad NFE
AF:
0.102
Gnomad OTH
AF:
0.112
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.133
AC:
19085
AN:
143826
Hom.:
1425
Cov.:
30
AF XY:
0.135
AC XY:
9448
AN XY:
70108
show subpopulations
Gnomad4 AFR
AF:
0.170
Gnomad4 AMR
AF:
0.110
Gnomad4 ASJ
AF:
0.107
Gnomad4 EAS
AF:
0.303
Gnomad4 SAS
AF:
0.194
Gnomad4 FIN
AF:
0.121
Gnomad4 NFE
AF:
0.102
Gnomad4 OTH
AF:
0.117
Alfa
AF:
0.106
Hom.:
568
Bravo
AF:
0.129
Asia WGS
AF:
0.225
AC:
782
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
5.2
Dann
Benign
0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8066154; hg19: chr17-27603086; API