rs7114011

Variant names:

• chr11-47789757-A-C
• rs7114011
• NM_015231.3:c.3410-1146T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-47789757-A-C
• chr11-47789757-A-G

Variant summary

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

The NM_015231.3(NUP160):​c.3410-1146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,752 control chromosomes in the GnomAD database, including 4,843 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 0.22 (4843 hom., cov: 31)
• Consequence: NUP160 NM_015231.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653
• Publications: 8 publications found

Genes affected

NUP160 (HGNC:18017): (nucleoporin 160) A structural constituent of nuclear pore. Involved in mRNA export from nucleus and nephron development. Part of nuclear pore outer ring. Colocalizes with kinetochore. Implicated in nephrotic syndrome type 19. [provided by Alliance of Genome Resources, Apr 2022]

NUP160 Gene-Disease associations (from GenCC):

• nephrotic syndrome, type 19

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• familial idiopathic steroid-resistant nephrotic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP160	NM_015231.3	c.3410-1146T>G		intron_variant	Intron 29 of 35	ENST00000378460.7	NP_056046.2
NUP160	NR_134636.3	n.3457-1146T>G		intron_variant	Intron 29 of 35

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP160	ENST00000378460.7	c.3410-1146T>G		intron_variant	Intron 29 of 35	1	NM_015231.3	ENSP00000367721.3
NUP160	ENST00000694866.1	c.3512-1146T>G		intron_variant	Intron 29 of 35			ENSP00000511549.1
NUP160	ENST00000530326.5	c.3404-1146T>G		intron_variant	Intron 29 of 33	5		ENSP00000433590.2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33944 AN: 151646 Hom.: 4844 Cov.: 31

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.224 AC: 33933 AN: 151752 Hom.: 4843 Cov.: 31 AF XY: 0.223 AC XY: 16549 AN XY: 74160

African (AFR) AF: 0.0559 AC: 2317 AN: 41450

American (AMR) AF: 0.223 AC: 3398 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1108 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1776 AN: 5158

South Asian (SAS) AF: 0.460 AC: 2212 AN: 4804

European-Finnish (FIN) AF: 0.209 AC: 2182 AN: 10456

Middle Eastern (MID) AF: 0.233 AC: 67 AN: 288

European-Non Finnish (NFE) AF: 0.296 AC: 20109 AN: 67908

Other (OTH) AF: 0.273 AC: 574 AN: 2106

Alfa AF: 0.181 Hom.: 567

Bravo AF: 0.212

Asia WGS AF: 0.402 AC: 1398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.51
PhyloP100		0.65
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: rs7114011; hg19: chr11-47811309;