chr11-47796758-C-T

Position:

• chr11-47796758-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_015231.3(NUP160):​c.3187+1021G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 152,284 control chromosomes in the GnomAD database, including 36 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 0.020 (36 hom., cov: 32)
• Consequence: NUP160 NM_015231.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0196 (2990/152284) while in subpopulation AFR AF= 0.0294 (1224/41574). AF 95% confidence interval is 0.0281. There are 36 homozygotes in gnomad4. There are 1391 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP160	NM_015231.3	c.3187+1021G>A		intron_variant		ENST00000378460.7	NP_056046.2
NUP160	NR_134636.3	n.3234+1021G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP160	ENST00000378460.7	c.3187+1021G>A		intron_variant		1	NM_015231.3	ENSP00000367721.3
NUP160	ENST00000694866.1	c.3289+1021G>A		intron_variant				ENSP00000511549.1
NUP160	ENST00000530326.5	c.3181+1021G>A		intron_variant		5		ENSP00000433590.2
NUP160	ENST00000528071.5	c.3187+1021G>A		intron_variant		5		ENSP00000432367.3

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2988 AN: 152166 Hom.: 36 Cov.: 32

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.00612

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0226

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

GnomAD4 genome AF: 0.0196 AC: 2990 AN: 152284 Hom.: 36 Cov.: 32 AF XY: 0.0187 AC XY: 1391 AN XY: 74472

Gnomad4 AFR AF: 0.0294

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00477

Gnomad4 FIN AF: 0.00612

Gnomad4 NFE AF: 0.0172

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0179 Hom.: 5

Bravo AF: 0.0216

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.16

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: rs58883118; hg19: chr11-47818310;