rs2271293

Variant names:

• chr16-67868167-G-A
• rs2271293
• NM_005796.3:c.100-173G>A

Variant summary

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

The NM_005796.3(NUTF2):​c.100-173G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,150 control chromosomes in the GnomAD database, including 1,069 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 0.11 (1069 hom., cov: 31)
• Consequence: NUTF2 NM_005796.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 98 publications found

Genes affected

NUTF2 (HGNC:13722): (nuclear transport factor 2) This gene encodes a cytosolic factor that facilitates protein transport into the nucleus. The encoded protein is required for nuclear import of the small Ras-like GTPase, Ran which is involved in numerous cellular processes. This protein also interacts with the nuclear pore complex glycoprotein p62. [provided by RefSeq, Apr 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTF2	NM_005796.3	c.100-173G>A		intron_variant	Intron 2 of 4	ENST00000219169.9	NP_005787.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTF2	ENST00000219169.9	c.100-173G>A		intron_variant	Intron 2 of 4	1	NM_005796.3	ENSP00000219169.4

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16921 AN: 152032 Hom.: 1068 Cov.: 31

Gnomad AFR AF: 0.0777

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0272

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.111 AC: 16923 AN: 152150 Hom.: 1069 Cov.: 31 AF XY: 0.115 AC XY: 8567 AN XY: 74376

African (AFR) AF: 0.0775 AC: 3219 AN: 41524

American (AMR) AF: 0.130 AC: 1984 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3472

East Asian (EAS) AF: 0.0274 AC: 142 AN: 5174

South Asian (SAS) AF: 0.180 AC: 869 AN: 4816

European-Finnish (FIN) AF: 0.168 AC: 1773 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8150 AN: 67980

Other (OTH) AF: 0.117 AC: 247 AN: 2114

Alfa AF: 0.117 Hom.: 4369

Bravo AF: 0.105

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.31
PhyloP100		-0.24
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: rs2271293; hg19: chr16-67902070;