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GeneBe

12-68689025-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_020401.4(NUP107):c.72G>A(p.Arg24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,611,062 control chromosomes in the GnomAD database, including 55,248 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4179 hom., cov: 32)
Exomes 𝑓: 0.26 ( 51069 hom. )

Consequence

NUP107
NM_020401.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0240
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 12-68689025-G-A is Benign according to our data. Variant chr12-68689025-G-A is described in ClinVar as [Benign]. Clinvar id is 1281812.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.024 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NUP107NM_020401.4 linkuse as main transcriptc.72G>A p.Arg24= synonymous_variant 2/28 ENST00000229179.9
NUP107XM_005269037.5 linkuse as main transcriptc.72G>A p.Arg24= synonymous_variant 2/27
NUP107NM_001330192.2 linkuse as main transcriptc.-44G>A 5_prime_UTR_variant 2/28

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NUP107ENST00000229179.9 linkuse as main transcriptc.72G>A p.Arg24= synonymous_variant 2/281 NM_020401.4 P1P57740-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.217
AC:
32965
AN:
152054
Hom.:
4177
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0850
Gnomad AMI
AF:
0.213
Gnomad AMR
AF:
0.264
Gnomad ASJ
AF:
0.254
Gnomad EAS
AF:
0.304
Gnomad SAS
AF:
0.223
Gnomad FIN
AF:
0.263
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.269
Gnomad OTH
AF:
0.250
GnomAD3 exomes
AF:
0.257
AC:
64481
AN:
250566
Hom.:
8679
AF XY:
0.258
AC XY:
34965
AN XY:
135482
show subpopulations
Gnomad AFR exome
AF:
0.0846
Gnomad AMR exome
AF:
0.283
Gnomad ASJ exome
AF:
0.253
Gnomad EAS exome
AF:
0.313
Gnomad SAS exome
AF:
0.233
Gnomad FIN exome
AF:
0.269
Gnomad NFE exome
AF:
0.270
Gnomad OTH exome
AF:
0.266
GnomAD4 exome
AF:
0.261
AC:
380935
AN:
1458890
Hom.:
51069
Cov.:
31
AF XY:
0.261
AC XY:
189379
AN XY:
725860
show subpopulations
Gnomad4 AFR exome
AF:
0.0787
Gnomad4 AMR exome
AF:
0.278
Gnomad4 ASJ exome
AF:
0.257
Gnomad4 EAS exome
AF:
0.291
Gnomad4 SAS exome
AF:
0.229
Gnomad4 FIN exome
AF:
0.270
Gnomad4 NFE exome
AF:
0.267
Gnomad4 OTH exome
AF:
0.260
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.217
AC:
32971
AN:
152172
Hom.:
4179
Cov.:
32
AF XY:
0.220
AC XY:
16338
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0850
Gnomad4 AMR
AF:
0.264
Gnomad4 ASJ
AF:
0.254
Gnomad4 EAS
AF:
0.303
Gnomad4 SAS
AF:
0.223
Gnomad4 FIN
AF:
0.263
Gnomad4 NFE
AF:
0.269
Gnomad4 OTH
AF:
0.252
Alfa
AF:
0.231
Hom.:
2745
Bravo
AF:
0.214
Asia WGS
AF:
0.279
AC:
969
AN:
3478
EpiCase
AF:
0.281
EpiControl
AF:
0.283

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -
Benign, criteria provided, single submitterclinical testingGeneDxOct 25, 2019- -
Galloway-Mowat syndrome 7 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 05, 2021- -
Nephrotic syndrome, type 11 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 05, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
Cadd
Benign
8.8
Dann
Benign
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
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.

Other links and lift over

dbSNP: rs2259588; hg19: chr12-69082805; COSMIC: COSV57496090; COSMIC: COSV57496090; API