Variant chr6-149731629-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_198887.3(NUP43):c.897G>A(p.Ser299Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000948 in 1,612,170 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0011 ( 1 hom., cov: 31)

Exomes 𝑓: 0.00093 ( 8 hom. )

Consequence

NUP43
NM_198887.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.115

Variant links:

Genes affected

NUP43 (HGNC:21182): (nucleoporin 43) Bidirectional transport of macromolecules between the cytoplasm and nucleus occurs through nuclear pore complexes (NPCs) embedded in the nuclear envelope. NPCs are composed of subcomplexes, and NUP43 is part of one such subcomplex, Nup107-160 (Loiodice et al., 2004 [PubMed 15146057]).[supplied by OMIM, Mar 2008]

NUP43 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 6-149731629-C-T is Benign according to our data. Variant chr6-149731629-C-T is described in ClinVar as [Benign]. Clinvar id is 778010.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.115 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP43	NM_198887.3 link	c.897G>A	p.Ser299Ser	synonymous_variant	7/8	ENST00000340413.7	NP_942590.1	Q8NFH3-1Q8TEA6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP43	ENST00000340413.7 link	c.897G>A	p.Ser299Ser	synonymous_variant	7/8	1	NM_198887.3	ENSP00000342262.2		Q8NFH3-1

Frequencies

GnomAD3 genomes

AF:

0.00110

AC:

166

AN:

151054

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000268

Gnomad AMI

AF:

0.00549

Gnomad AMR

AF:

0.00132

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000625

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0321

Gnomad NFE

AF:

0.000781

Gnomad OTH

AF:

0.00193

GnomAD3 exomes

AF:

0.00138

AC:

347

AN:

251126

Hom.:

AF XY:

0.00155

AC XY:

210

AN XY:

135736

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.00101

Gnomad ASJ exome

AF:

0.0168

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000458

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.000933

Gnomad OTH exome

AF:

0.00342

GnomAD4 exome

AF:

0.000932

AC:

1362

AN:

1461044

Hom.:

Cov.:

AF XY:

0.000985

AC XY:

716

AN XY:

726836

show subpopulations

Gnomad4 AFR exome

AF:

0.000807

Gnomad4 AMR exome

AF:

0.00110

Gnomad4 ASJ exome

AF:

0.0173

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000418

Gnomad4 FIN exome

AF:

0.0000562

Gnomad4 NFE exome

AF:

0.000517

Gnomad4 OTH exome

AF:

0.00244

GnomAD4 genome

AF:

0.00111

AC:

167

AN:

151126

Hom.:

Cov.:

AF XY:

0.00106

AC XY:

AN XY:

73690

show subpopulations

Gnomad4 AFR

AF:

0.000267

Gnomad4 AMR

AF:

0.00132

Gnomad4 ASJ

AF:

0.0173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00105

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000781

Gnomad4 OTH

AF:

0.00191

Alfa

AF:

0.00213

Hom.:

Bravo

AF:

0.00118

EpiCase

AF:

0.00185

EpiControl

AF:

0.00261

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

7.0

DANN

Benign

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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