chr17-29269188-C-T

Variant names:

• chr17-29269188-C-T
• rs10491212
• NM_020772.3:c.2003-1658G>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.2003-1658G>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
• Publications: 2 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=-0.89).
• 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 rank	MANE	Protein	UniProt
NUFIP2	NM_020772.3	c.2003-1658G>A		intron_variant	Intron 2 of 3	ENST00000225388.9	NP_065823.1
NUFIP2	XM_017024896.3	c.1526-1658G>A		intron_variant	Intron 2 of 3		XP_016880385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUFIP2	ENST00000225388.9	c.2003-1658G>A		intron_variant	Intron 2 of 3	1	NM_020772.3	ENSP00000225388.3
NUFIP2	ENST00000579665.1	c.278-1658G>A		intron_variant	Intron 1 of 2	1		ENSP00000463450.1

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

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: 34 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11275 AN: 67980

Other (OTH) AF: 0.197 AC: 416 AN: 2110

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.21
PhyloP100		-0.21
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: rs10491212; hg19: chr17-27596206;