11-47789757-A-C

Position:

• chr11-47789757-A-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NUP160	NM_015231.3	c.3410-1146T>G		intron_variant		ENST00000378460.7	NP_056046.2
NUP160	NR_134636.3	n.3457-1146T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP160	ENST00000378460.7	c.3410-1146T>G		intron_variant		1	NM_015231.3	ENSP00000367721	P1
NUP160	ENST00000530326.5	c.3405-1146T>G		intron_variant		5		ENSP00000433590
NUP160	ENST00000694866.1	c.3512-1146T>G		intron_variant				ENSP00000511549

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

Gnomad4 AFR AF: 0.0559

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.273

Alfa AF: 0.185 Hom.: 562

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

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: rs7114011; hg19: chr11-47811309;