Genetic Variant NM_020772.3:c.2003-1658G>A (chr17-29269188-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206

Publications

2 publications found

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]

NUFIP2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_020772.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020772.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUFIP2	NM_020772.3	MANE Select	c.2003-1658G>A		intron	N/A	NP_065823.1	Q7Z417-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NUFIP2	ENST00000225388.9	TSL:1 MANE Select	c.2003-1658G>A	intron	N/A	ENSP00000225388.3	Q7Z417-1
NUFIP2	ENST00000579665.1	TSL:1	c.278-1658G>A	intron	N/A	ENSP00000463450.1	Q7Z417-2
NUFIP2	ENST00000934592.1		c.2003-4597G>A	intron	N/A	ENSP00000604651.1

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

33989

AN:

151936

Hom.:

4253

Cov.:

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.:

AF XY:

0.227

AC XY:

16843

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.330

AC:

13666

AN:

41460

American (AMR)

AF:

0.168

AC:

2574

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

513

AN:

3470

East Asian (EAS)

AF:

0.333

AC:

1721

AN:

5170

South Asian (SAS)

AF:

0.353

AC:

1702

AN:

4822

European-Finnish (FIN)

AF:

0.183

AC:

1932

AN:

10556

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11275

AN:

67980

Other (OTH)

AF:

0.197

AC:

416

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1335

2670

4005

5340

6675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.190

Hom.:

1156

Bravo

AF:

0.224

Asia WGS

AF:

0.362

AC:

1256

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.8

(source)

DANN

Benign

0.21

PhyloP100

-0.21

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over