X-102326266-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong 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

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

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• 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 id is 3388541.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.509 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXF2	NM_022053.4	c.1779C>T	p.Cys593Cys	synonymous_variant	Exon 22 of 23	ENST00000625106.4	NP_071336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NXF2	ENST00000625106.4	c.1779C>T	p.Cys593Cys	synonymous_variant	Exon 22 of 23	1	NM_022053.4	ENSP00000485586.2
NXF2	ENST00000604790.2	c.1779C>T	p.Cys593Cys	synonymous_variant	Exon 20 of 21	1		ENSP00000474598.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.000278 AC: 6 AN: 21618 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4206

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 SAS 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

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

NXF2: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	9.4
DANN	Benign	0.17

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: rs781918360; hg19: chrX-101581180;