11-47804538-A-C

Variant names:

• chr11-47804538-A-C
• rs11039402
• NM_015231.3:c.2574+11T>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_015231.3(NUP160):​c.2574+11T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 1,512,470 control chromosomes in the GnomAD database, including 144,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.35 (10568 hom., cov: 33)
  • Exomes 𝑓: 0.44 (134275 hom.)
• Consequence: NUP160 NM_015231.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.173
• Publications: 10 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]

RNA5SP340 (HGNC:43240): (RNA, 5S ribosomal pseudogene 340)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant 11-47804538-A-C is Benign according to our data. Variant chr11-47804538-A-C is described in ClinVar as Benign. ClinVar VariationId is 1327015.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015231.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP160	NM_015231.3	MANE Select	c.2574+11T>G		intron	N/A	NP_056046.2
	NUP160	NR_134636.3		n.2621+11T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP160	ENST00000378460.7	TSL:1 MANE Select	c.2574+11T>G		intron	N/A	ENSP00000367721.3
	NUP160	ENST00000527750.1	TSL:3	n.169T>G		non_coding_transcript_exon	Exon 2 of 2
	NUP160	ENST00000694866.1		c.2676+11T>G		intron	N/A	ENSP00000511549.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52688 AN: 152034 Hom.: 10569 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.400

GnomAD2 exomes AF: 0.407 AC: 74952 AN: 184372 AF XY: 0.422

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.238

Gnomad ASJ exome AF: 0.478

Gnomad EAS exome AF: 0.379

Gnomad FIN exome AF: 0.348

Gnomad NFE exome AF: 0.453

Gnomad OTH exome AF: 0.425

GnomAD4 exome AF: 0.437 AC: 594823 AN: 1360318 Hom.: 134275 Cov.: 24 AF XY: 0.441 AC XY: 298505 AN XY: 676610

African (AFR) AF: 0.132 AC: 3719 AN: 28098

American (AMR) AF: 0.260 AC: 6761 AN: 26028

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 11596 AN: 23706

East Asian (EAS) AF: 0.311 AC: 10655 AN: 34236

South Asian (SAS) AF: 0.529 AC: 37623 AN: 71110

European-Finnish (FIN) AF: 0.360 AC: 19031 AN: 52850

Middle Eastern (MID) AF: 0.437 AC: 2430 AN: 5566

European-Non Finnish (NFE) AF: 0.451 AC: 478652 AN: 1062254

Other (OTH) AF: 0.431 AC: 24356 AN: 56470

GnomAD4 genome AF: 0.346 AC: 52682 AN: 152152 Hom.: 10568 Cov.: 33 AF XY: 0.343 AC XY: 25505 AN XY: 74392

African (AFR) AF: 0.148 AC: 6161 AN: 41538

American (AMR) AF: 0.326 AC: 4988 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1702 AN: 3464

East Asian (EAS) AF: 0.392 AC: 2028 AN: 5180

South Asian (SAS) AF: 0.519 AC: 2506 AN: 4826

European-Finnish (FIN) AF: 0.340 AC: 3599 AN: 10578

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30525 AN: 67978

Other (OTH) AF: 0.396 AC: 833 AN: 2104

Alfa AF: 0.300 Hom.: 3816

Bravo AF: 0.333

Asia WGS AF: 0.466 AC: 1620 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Nephrotic syndrome, type 19 Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.17
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs11039402; hg19: chr11-47826090; COSMIC: COSV65854472; COSMIC: COSV65854472;