12-68688816-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020401.4(NUP107):c.9-146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 498,500 control chromosomes in the GnomAD database, including 16,048 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (3726 hom., cov: 32)
  • Exomes 𝑓: 0.25 (12322 hom.)
• Consequence: NUP107 NM_020401.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.273

Genes affected

NUP107 (HGNC:29914): (nucleoporin 107) This gene encodes a member of the nucleoporin family. The protein is localized to the nuclear rim and is an essential component of the nuclear pore complex (NPC). All molecules entering or leaving the nucleus either diffuse through or are actively transported by the NPC. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 12-68688816-G-A is Benign according to our data. Variant chr12-68688816-G-A is described in ClinVar as [Benign]. Clinvar id is 1260392.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP107	NM_020401.4	c.9-146G>A		intron_variant		ENST00000229179.9
NUP107	NM_001330192.2	c.-107-146G>A		intron_variant
NUP107	XM_005269037.5	c.9-146G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP107	ENST00000229179.9	c.9-146G>A		intron_variant		1	NM_020401.4	P1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29919 AN: 152002 Hom.: 3732 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.255 AC: 88273 AN: 346380 Hom.: 12322 AF XY: 0.265 AC XY: 48138 AN XY: 181644

Gnomad4 AFR exome AF: 0.0733

Gnomad4 AMR exome AF: 0.199

Gnomad4 ASJ exome AF: 0.411

Gnomad4 EAS exome AF: 0.265

Gnomad4 SAS exome AF: 0.460

Gnomad4 FIN exome AF: 0.194

Gnomad4 NFE exome AF: 0.242

Gnomad4 OTH exome AF: 0.249

GnomAD4 genome AF: 0.197 AC: 29916 AN: 152120 Hom.: 3726 Cov.: 32 AF XY: 0.200 AC XY: 14903 AN XY: 74368

Gnomad4 AFR AF: 0.0690

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.212

Alfa AF: 0.236 Hom.: 7542

Bravo AF: 0.187

Asia WGS AF: 0.328 AC: 1145 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	8.2
Dann	Benign	0.70

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: rs2303042; hg19: chr12-69082596;