Genetic Variant NUP107-DT:n.822+256G>A (chr12-68686678-C-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The ENST00000502102.2(NUP107-DT):n.822+256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 211,878 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0096 ( 14 hom., cov: 33)

Exomes 𝑓: 0.012 ( 9 hom. )

Consequence

NUP107-DT
ENST00000502102.2 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.22

Publications

1 publications found

Variant links:

Genes affected

NUP107-DT (HGNC:55587): (NUP107 divergent transcript [Source:HGNC Symbol%3BAcc:HGNC:55587])

NUP107-DT links:

LOC100507250 (HGNC:):

LOC100507250 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 12-68686678-C-T is Benign according to our data. Variant chr12-68686678-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1320404.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 14 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502102.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100507250	NR_038930.1		n.123+59G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
NUP107-DT	ENST00000502102.2	TSL:1	n.822+256G>A	intron	N/A
NUP107-DT	ENST00000433116.2	TSL:2	n.101+59G>A	intron	N/A
NUP107-DT	ENST00000500695.2	TSL:5	n.123+59G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00963

AC:

1466

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00273

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.00530

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.0137

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0151

Gnomad OTH

AF:

0.0105

GnomAD4 exome

AF:

0.0124

AC:

739

AN:

59514

Hom.:

AF XY:

0.0127

AC XY:

389

AN XY:

30662

show subpopulations

African (AFR)

AF:

0.00186

AC:

AN:

2146

American (AMR)

AF:

0.00736

AC:

AN:

2580

Ashkenazi Jewish (ASJ)

AF:

0.0137

AC:

AN:

2038

East Asian (EAS)

AF:

0.000322

AC:

AN:

3108

South Asian (SAS)

AF:

0.00539

AC:

AN:

5006

European-Finnish (FIN)

AF:

0.0147

AC:

AN:

3056

Middle Eastern (MID)

AF:

0.00338

AC:

AN:

296

European-Non Finnish (NFE)

AF:

0.0150

AC:

564

AN:

37534

Other (OTH)

AF:

0.0133

AC:

AN:

3750

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

110

146

183

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00962

AC:

1465

AN:

152364

Hom.:

Cov.:

AF XY:

0.00921

AC XY:

686

AN XY:

74506

show subpopulations

African (AFR)

AF:

0.00272

AC:

113

AN:

41586

American (AMR)

AF:

0.00529

AC:

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0107

AC:

AN:

3472

East Asian (EAS)

AF:

0.000385

AC:

AN:

5192

South Asian (SAS)

AF:

0.00538

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0137

AC:

145

AN:

10620

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0151

AC:

1025

AN:

68040

Other (OTH)

AF:

0.0104

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

161

242

322

403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00587

Hom.:

Bravo

AF:

0.00909

Asia WGS

AF:

0.00433

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

4.7

(source)

DANN

Benign

0.83

PhyloP100

-1.2

PromoterAI

-0.38

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over