17-29269188-C-T

Position:

• chr17-29269188-C-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

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=-0.89).
• 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	Protein	UniProt
NUFIP2	NM_020772.3	c.2003-1658G>A		intron_variant		ENST00000225388.9	NP_065823.1
NUFIP2	XM_017024896.3	c.1526-1658G>A		intron_variant			XP_016880385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUFIP2	ENST00000225388.9	c.2003-1658G>A		intron_variant		1	NM_020772.3	ENSP00000225388	P1
NUFIP2	ENST00000579665.1	c.278-1658G>A		intron_variant		1		ENSP00000463450

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33989 AN: 151936 Hom.: 4253 Cov.: 32

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

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

Other links and lift over

dbSNP: rs10491212; hg19: chr17-27596206;