rs9350051

Variant names:

• chr6-17614721-A-C
• rs9350051
• ENST00000874440.1:c.*1376T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-17614721-A-C
• chr6-17614721-A-G
• chr6-17614721-A-T

Variant summary

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

The ENST00000874440.1(NUP153):​c.*1376T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 150,428 control chromosomes in the GnomAD database, including 18,128 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 0.48 (18128 hom., cov: 27)
• Consequence: NUP153 ENST00000874440.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000874440.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP153	ENST00000874440.1		c.*1376T>G		3_prime_UTR	Exon 21 of 21	ENSP00000544499.1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 72763 AN: 150312 Hom.: 18113 Cov.: 27

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.484 AC: 72817 AN: 150428 Hom.: 18128 Cov.: 27 AF XY: 0.484 AC XY: 35484 AN XY: 73310

African (AFR) AF: 0.448 AC: 18319 AN: 40890

American (AMR) AF: 0.531 AC: 7979 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2178 AN: 3462

East Asian (EAS) AF: 0.554 AC: 2803 AN: 5056

South Asian (SAS) AF: 0.684 AC: 3268 AN: 4776

European-Finnish (FIN) AF: 0.359 AC: 3638 AN: 10138

Middle Eastern (MID) AF: 0.757 AC: 218 AN: 288

European-Non Finnish (NFE) AF: 0.483 AC: 32735 AN: 67796

Other (OTH) AF: 0.532 AC: 1109 AN: 2084

Alfa AF: 0.503 Hom.: 32801

Bravo AF: 0.490

Asia WGS AF: 0.621 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.70
PhyloP100		-0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9350051; hg19: chr6-17614952;