rs7198357

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-67850716-C-A
• chr16-67850716-C-G
• chr16-67850716-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005796.3(NUTF2):​c.-30+3731C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005796.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTF2	NM_005796.3	MANE Select	c.-30+3731C>A		intron	N/A	NP_005787.1	P61970
	NUTF2	NM_001322038.2		c.-120+3731C>A		intron	N/A	NP_001308967.1	P61970
	NUTF2	NM_001322039.2		c.-30+3260C>A		intron	N/A	NP_001308968.1	P61970

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTF2	ENST00000219169.9	TSL:1 MANE Select	c.-30+3731C>A		intron	N/A	ENSP00000219169.4	P61970
	NUTF2	ENST00000570026.2	TSL:2	c.-30+3260C>A		intron	N/A	ENSP00000515106.1	A0A8V8TR28
	NUTF2	ENST00000700610.1		c.-30+3731C>A		intron	N/A	ENSP00000515098.1	A0A8V8TR28

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 7295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.4
DANN	Benign	0.44
PhyloP100		0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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;