rs8614

Positions:

• chr17-29261788-C-A
• chr17-29261788-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020772.3(NUFIP2):​c.*2751G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,492 control chromosomes in the GnomAD database, including 2,681 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 (2678 hom., cov: 32)
  • Exomes 𝑓: 0.20 (3 hom.)
• Consequence: NUFIP2 NM_020772.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUFIP2	NM_020772.3	c.*2751G>T		3_prime_UTR_variant	4/4	ENST00000225388.9	NP_065823.1
NUFIP2	XM_017024896.3	c.*2751G>T		3_prime_UTR_variant	4/4		XP_016880385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUFIP2	ENST00000225388.9	c.*2751G>T		3_prime_UTR_variant	4/4	1	NM_020772.3	ENSP00000225388.3

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23987 AN: 151940 Hom.: 2676 Cov.: 32

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.196 AC: 85 AN: 434 Hom.: 3 Cov.: 0 AF XY: 0.183 AC XY: 48 AN XY: 262

Gnomad4 FIN exome AF: 0.197

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.158 AC: 23993 AN: 152058 Hom.: 2678 Cov.: 32 AF XY: 0.159 AC XY: 11787 AN XY: 74332

Gnomad4 AFR AF: 0.0413

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.184

Alfa AF: 0.180 Hom.: 3477

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	14
DANN	Benign	0.81

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

Other links and lift over

dbSNP: rs8614; hg19: chr17-27588806;