Genetic Variant NUP107:c.9-73A>G (chr12-68688889-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020401.4(NUP107):c.9-73A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,151,510 control chromosomes in the GnomAD database, including 61,816 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 8621 hom., cov: 32)

Exomes 𝑓: 0.32 ( 53195 hom. )

Consequence

NUP107
NM_020401.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.26

Variant links:

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]

NUP107 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 12-68688889-A-G is Benign according to our data. Variant chr12-68688889-A-G is described in ClinVar as [Benign]. Clinvar id is 1272631.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
NUP107	NM_020401.4 link	c.9-73A>G	intron_variant	Intron 1 of 27	ENST00000229179.9	NP_065134.1	P57740-1
NUP107	NM_001330192.2 link	c.-107-73A>G	intron_variant	Intron 1 of 27		NP_001317121.1	P57740-2
NUP107	XM_005269037.5 link	c.9-73A>G	intron_variant	Intron 1 of 26		XP_005269094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP107	ENST00000229179.9 link	c.9-73A>G		intron_variant	Intron 1 of 27	1	NM_020401.4	ENSP00000229179.4		P57740-1

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50882

AN:

151854

Hom.:

8613

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.383

Gnomad MID

AF:

0.366

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.344

GnomAD4 exome

AF:

0.325

AC:

324438

AN:

999538

Hom.:

53195

AF XY:

0.324

AC XY:

165376

AN XY:

511022

show subpopulations

Gnomad4 AFR exome

AF:

0.329

Gnomad4 AMR exome

AF:

0.321

Gnomad4 ASJ exome

AF:

0.317

Gnomad4 EAS exome

AF:

0.282

Gnomad4 SAS exome

AF:

0.310

Gnomad4 FIN exome

AF:

0.384

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.329

GnomAD4 genome

AF:

0.335

AC:

50920

AN:

151972

Hom.:

8621

Cov.:

AF XY:

0.339

AC XY:

25169

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.335

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.328

Gnomad4 EAS

AF:

0.302

Gnomad4 SAS

AF:

0.309

Gnomad4 FIN

AF:

0.383

Gnomad4 NFE

AF:

0.333

Gnomad4 OTH

AF:

0.345

Alfa

AF:

0.336

Hom.:

2386

Bravo

AF:

0.332

Asia WGS

AF:

0.326

AC:

1132

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Aug 20, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Jul 15, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 54% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 50. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.023

DANN

Benign

0.62

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over