NM_005124.4:c.334+1515G>C

Variant names:

• chr6-17686881-C-G
• rs9383311
• NM_005124.4:c.334+1515G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_005124.4(NUP153):​c.334+1515G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 (13830 hom., cov: 12)
  • Failed GnomAD Quality Control
• Consequence: NUP153 NM_005124.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 3 publications found

Genes affected

NUP153 (HGNC:8062): (nucleoporin 153) Nuclear pore complexes regulate the transport of macromolecules between the nucleus and cytoplasm. They are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. Nucleoporins are glycoproteins found in nuclear pores and contain characteristic pentapeptide XFXFG repeats as well as O-linked N-acetylglucosamine residues oriented towards the cytoplasm. The protein encoded by this gene has three distinct domains: a N-terminal region containing a pore targeting and an RNA-binding domain domain, a central region containing multiple zinc finger motifs, and a C-terminal region containing multiple XFXFG repeats. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP153	NM_005124.4	c.334+1515G>C		intron_variant	Intron 2 of 21	ENST00000262077.3	NP_005115.2
NUP153	NM_001278209.2	c.334+1515G>C		intron_variant	Intron 2 of 22		NP_001265138.1
NUP153	NM_001278210.2	c.334+1515G>C		intron_variant	Intron 2 of 20		NP_001265139.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP153	ENST00000262077.3	c.334+1515G>C		intron_variant	Intron 2 of 21	1	NM_005124.4	ENSP00000262077.3
NUP153	ENST00000613258.4	c.334+1515G>C		intron_variant	Intron 2 of 20	1		ENSP00000478627.1
NUP153	ENST00000537253.5	c.334+1515G>C		intron_variant	Intron 2 of 22	2		ENSP00000444029.1

Frequencies

GnomAD3 genomes AF: 0.648 AC: 58723 AN: 90674 Hom.: 13825 Cov.: 12

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.666

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.648 AC: 58763 AN: 90748 Hom.: 13830 Cov.: 12 AF XY: 0.648 AC XY: 28061 AN XY: 43306

African (AFR) AF: 0.590 AC: 11075 AN: 18766

American (AMR) AF: 0.669 AC: 6277 AN: 9378

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2085 AN: 2876

East Asian (EAS) AF: 0.683 AC: 2273 AN: 3328

South Asian (SAS) AF: 0.750 AC: 2422 AN: 3228

European-Finnish (FIN) AF: 0.593 AC: 2766 AN: 4666

Middle Eastern (MID) AF: 0.811 AC: 193 AN: 238

European-Non Finnish (NFE) AF: 0.655 AC: 30285 AN: 46254

Other (OTH) AF: 0.670 AC: 886 AN: 1322

Alfa AF: 0.274 Hom.: 644

Bravo AF: 0.449

Asia WGS AF: 0.600 AC: 1978 AN: 3302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.70
DANN	Benign	0.36
PhyloP100		-2.8
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: rs9383311; hg19: chr6-17687112;