Variant chr12-68686948-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000502102.2(NUP107-DT):n.808A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,195,324 control chromosomes in the GnomAD database, including 67,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 8764 hom., cov: 34)

Exomes 𝑓: 0.33 ( 58425 hom. )

Consequence

NUP107-DT
ENST00000502102.2 non_coding_transcript_exon

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.124

Variant links:

Genes affected

NUP107-DT (HGNC:):

NUP107-DT links:

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=-0.87).

BP6

Variant 12-68686948-T-G is Benign according to our data. Variant chr12-68686948-T-G is described in ClinVar as [Benign]. Clinvar id is 1269166.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
	use as main transcript	n.68686948T>G	intergenic_region
NUP107	NM_020401.4 linkuse as main transcript	c.-118T>G	upstream_gene_variant	ENST00000229179.9	NP_065134.1	P57740-1
NUP107	NM_001330192.2 linkuse as main transcript	c.-233T>G	upstream_gene_variant		NP_001317121.1	P57740-2
NUP107	XM_005269037.5 linkuse as main transcript	c.-118T>G	upstream_gene_variant		XP_005269094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP107	ENST00000229179.9 linkuse as main transcript	c.-118T>G		upstream_gene_variant		1	NM_020401.4	ENSP00000229179.4		P57740-1

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51377

AN:

152036

Hom.:

8758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.384

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.348

GnomAD4 exome

AF:

0.332

AC:

346360

AN:

1043170

Hom.:

58425

Cov.:

AF XY:

0.331

AC XY:

176866

AN XY:

534676

show subpopulations

Gnomad4 AFR exome

AF:

0.337

Gnomad4 AMR exome

AF:

0.340

Gnomad4 ASJ exome

AF:

0.323

Gnomad4 EAS exome

AF:

0.298

Gnomad4 SAS exome

AF:

0.306

Gnomad4 FIN exome

AF:

0.390

Gnomad4 NFE exome

AF:

0.331

Gnomad4 OTH exome

AF:

0.338

GnomAD4 genome

AF:

0.338

AC:

51418

AN:

152154

Hom.:

8764

Cov.:

AF XY:

0.342

AC XY:

25441

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.343

Gnomad4 AMR

AF:

0.338

Gnomad4 ASJ

AF:

0.329

Gnomad4 EAS

AF:

0.318

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.384

Gnomad4 NFE

AF:

0.334

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.340

Hom.:

8160

Bravo

AF:

0.335

Asia WGS

AF:

0.331

AC:

1150

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 20, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jul 15, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 44% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 41. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.6

DANN

Benign

0.67

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