17-29276068-C-T

Variant names:

• chr17-29276068-C-T
• rs8066154
• NM_020772.3:c.2003-8538G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUFIP2	NM_020772.3	MANE Select	c.2003-8538G>A		intron	N/A	NP_065823.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUFIP2	ENST00000225388.9	TSL:1 MANE Select	c.2003-8538G>A		intron	N/A	ENSP00000225388.3
	NUFIP2	ENST00000579665.1	TSL:1	c.278-8538G>A		intron	N/A	ENSP00000463450.1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 19068 AN: 143712 Hom.: 1423 Cov.: 30

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

African (AFR) AF: 0.170 AC: 6506 AN: 38236

American (AMR) AF: 0.110 AC: 1606 AN: 14634

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 362 AN: 3388

East Asian (EAS) AF: 0.303 AC: 1533 AN: 5052

South Asian (SAS) AF: 0.194 AC: 815 AN: 4200

European-Finnish (FIN) AF: 0.121 AC: 1211 AN: 9996

Middle Eastern (MID) AF: 0.0432 AC: 12 AN: 278

European-Non Finnish (NFE) AF: 0.102 AC: 6632 AN: 65140

Other (OTH) AF: 0.117 AC: 235 AN: 2014

Alfa AF: 0.107 Hom.: 618

Bravo AF: 0.129

Asia WGS AF: 0.225 AC: 782 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	5.2
DANN	Benign	0.84
PhyloP100		1.1
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

Other links and lift over

dbSNP: rs8066154; hg19: chr17-27603086;