16-67850716-C-T

Variant names:

• chr16-67850716-C-T
• rs7198357
• NM_005796.3:c.-30+3731C>T

Variant summary

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

The NM_005796.3(NUTF2):​c.-30+3731C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,012 control chromosomes in the GnomAD database, including 9,203 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 0.29 (9203 hom., cov: 31)
• Consequence: NUTF2 NM_005796.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 19 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTF2	NM_005796.3	c.-30+3731C>T		intron_variant	Intron 1 of 4	ENST00000219169.9	NP_005787.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTF2	ENST00000219169.9	c.-30+3731C>T		intron_variant	Intron 1 of 4	1	NM_005796.3	ENSP00000219169.4

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44278 AN: 151894 Hom.: 9174 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.292 AC: 44355 AN: 152012 Hom.: 9203 Cov.: 31 AF XY: 0.290 AC XY: 21545 AN XY: 74306

African (AFR) AF: 0.590 AC: 24424 AN: 41404

American (AMR) AF: 0.231 AC: 3527 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3470

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5180

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4816

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11588 AN: 67980

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.208 Hom.: 7295

Bravo AF: 0.303

Asia WGS AF: 0.210 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.6
DANN	Benign	0.46
PhyloP100		0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs7198357; hg19: chr16-67884619;