17-29280244-A-G

Position:

• chr17-29280244-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020772.3(NUFIP2):​c.2002+5748T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,334 control chromosomes in the GnomAD database, including 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 0.049 (261 hom., cov: 32)
• Consequence: NUFIP2 NM_020772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUFIP2	NM_020772.3	c.2002+5748T>C		intron_variant		ENST00000225388.9
NUFIP2	XM_017024896.3	c.1525+5748T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUFIP2	ENST00000225388.9	c.2002+5748T>C		intron_variant		1	NM_020772.3	P1
NUFIP2	ENST00000579665.1	c.278-12714T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0491 AC: 7467 AN: 152216 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0608

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.0483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0491 AC: 7478 AN: 152334 Hom.: 261 Cov.: 32 AF XY: 0.0518 AC XY: 3857 AN XY: 74488

Gnomad4 AFR AF: 0.0610

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0483

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0271 Hom.: 25

Bravo AF: 0.0455

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.48
DANN	Benign	0.72

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: rs10491211; hg19: chr17-27607262;