rs10491212

Variant summary

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

The NM_020772.3(NUFIP2):​c.2003-1658G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,056 control chromosomes in the GnomAD database, including 4,261 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 0.22 ( 4261 hom., cov: 32)

Consequence

NUFIP2
NM_020772.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NUFIP2NM_020772.3 linkuse as main transcriptc.2003-1658G>A intron_variant ENST00000225388.9
NUFIP2XM_017024896.3 linkuse as main transcriptc.1526-1658G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NUFIP2ENST00000225388.9 linkuse as main transcriptc.2003-1658G>A intron_variant 1 NM_020772.3 P1Q7Z417-1
NUFIP2ENST00000579665.1 linkuse as main transcriptc.278-1658G>A intron_variant 1 Q7Z417-2

Frequencies

GnomAD3 genomes
AF:
0.224
AC:
33989
AN:
151936
Hom.:
4253
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.329
Gnomad AMI
AF:
0.226
Gnomad AMR
AF:
0.169
Gnomad ASJ
AF:
0.148
Gnomad EAS
AF:
0.332
Gnomad SAS
AF:
0.354
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.166
Gnomad OTH
AF:
0.194
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.224
AC:
34039
AN:
152056
Hom.:
4261
Cov.:
32
AF XY:
0.227
AC XY:
16843
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.330
Gnomad4 AMR
AF:
0.168
Gnomad4 ASJ
AF:
0.148
Gnomad4 EAS
AF:
0.333
Gnomad4 SAS
AF:
0.353
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.166
Gnomad4 OTH
AF:
0.197
Alfa
AF:
0.186
Hom.:
897
Bravo
AF:
0.224
Asia WGS
AF:
0.362
AC:
1256
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.8
DANN
Benign
0.21

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: rs10491212; hg19: chr17-27596206; API