X-102326266-C-T

Variant names:

• chrX-102326266-C-T
• rs781918360
• NM_022053.4:c.1779C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Moderate BP6_Moderate BP7

The NM_022053.4(NXF2):​c.1779C>T​(p.Cys593Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: NXF2 NM_022053.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.509
• Publications: 1 publications found

Genes affected

NXF2 (HGNC:8072): (nuclear RNA export factor 2) This gene encodes a member of a family of nuclear RNA export proteins. The encoded protein is associated with the nuclear envelope and aids in the export of mRNAs. There is a closely related paralog of this gene located adjacent on chromosome X and on the opposite strand. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.068).
• BP6: Variant X-102326266-C-T is Benign according to our data. Variant chrX-102326266-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3388541.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.509 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022053.4. 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
	NXF2	NM_022053.4	MANE Select	c.1779C>T	p.Cys593Cys	synonymous	Exon 22 of 23	NP_071336.1	Q9GZY0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXF2	ENST00000625106.4	TSL:1 MANE Select	c.1779C>T	p.Cys593Cys	synonymous	Exon 22 of 23	ENSP00000485586.2	Q9GZY0
	NXF2	ENST00000604790.2	TSL:1	c.1779C>T	p.Cys593Cys	synonymous	Exon 20 of 21	ENSP00000474598.2	Q9GZY0

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.000278 AC: 6 AN: 21618 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000358

Gnomad ASJ exome AF: 0.00127

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000377

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.000650 Hom.: 0

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	9.4
DANN	Benign	0.17
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism

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: rs781918360; hg19: chrX-101581180;