rs2271293

chr16-67868167-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NUTF2	NM_005796.3	c.100-173G>A		intron_variant		ENST00000219169.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUTF2	ENST00000219169.9	c.100-173G>A		intron_variant		1	NM_005796.3	P1

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

Gnomad4 AFR AF: 0.0775

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0274

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.117

Alfa AF: 0.120 Hom.: 1969

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

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: rs2271293; hg19: chr16-67902070;