Genetic Variant NM_001396030.1:c.930G>A (chr16-28456739-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001396030.1(NPIPB7):c.930G>A(p.Pro310Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00029 ( 2 hom., cov: 8)

Exomes 𝑓: 0.00032 ( 31 hom. )

Failed GnomAD Quality Control

Consequence

NPIPB7
NM_001396030.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.42

Publications

0 publications found

Variant links:

Genes affected

NPIPB7 (HGNC:33832): (nuclear pore complex interacting protein family member B7) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPIPB7 links:

ENSG00000261832 (HGNC:):

ENSG00000261832 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 16-28456739-C-T is Benign according to our data. Variant chr16-28456739-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3250560.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.42 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396030.1. 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
	NPIPB7	NM_001396030.1	MANE Select	c.930G>A	p.Pro310Pro	synonymous	Exon 7 of 7	NP_001382959.1	O75200

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NPIPB7	ENST00000452313.6	TSL:5 MANE Select	c.930G>A	p.Pro310Pro	synonymous	Exon 7 of 7	ENSP00000405348.1	O75200
ENSG00000261832	ENST00000637378.1	TSL:5	c.1092G>A	p.Pro364Pro	synonymous	Exon 10 of 10	ENSP00000490831.1	A0A1B0GW90
NPIPB7	ENST00000435324.4	TSL:5	c.948G>A	p.Pro316Pro	synonymous	Exon 7 of 7	ENSP00000415207.4	I3L0I5

Frequencies

GnomAD3 genomes

AF:

0.000273

AC:

AN:

58578

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000246

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000200

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000524

Gnomad SAS

AF:

0.000601

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000293

Gnomad OTH

AF:

0.00134

GnomAD2 exomes

AF:

0.000209

AC:

AN:

19146

AF XY:

0.000206

show subpopulations

Gnomad AFR exome

AF:

0.000575

Gnomad AMR exome

AF:

0.000261

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000634

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000316

AC:

172

AN:

544378

Hom.:

Cov.:

AF XY:

0.000370

AC XY:

107

AN XY:

289142

show subpopulations

African (AFR)

AF:

0.000796

AC:

AN:

16332

American (AMR)

AF:

0.000734

AC:

AN:

23158

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16698

East Asian (EAS)

AF:

0.000103

AC:

AN:

29092

South Asian (SAS)

AF:

0.000531

AC:

AN:

56516

European-Finnish (FIN)

AF:

0.000265

AC:

AN:

26388

Middle Eastern (MID)

AF:

0.00290

AC:

AN:

2416

European-Non Finnish (NFE)

AF:

0.000200

AC:

AN:

345162

Other (OTH)

AF:

0.000909

AC:

AN:

28616

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000290

AC:

AN:

58594

Hom.:

Cov.:

AF XY:

0.000289

AC XY:

AN XY:

27686

show subpopulations

African (AFR)

AF:

0.000307

AC:

AN:

16288

American (AMR)

AF:

0.000200

AC:

AN:

4990

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1616

East Asian (EAS)

AF:

0.000524

AC:

AN:

1910

South Asian (SAS)

AF:

0.000602

AC:

AN:

1660

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3378

Middle Eastern (MID)

AF:

0.00

AC:

AN:

146

European-Non Finnish (NFE)

AF:

0.000293

AC:

AN:

27288

Other (OTH)

AF:

0.00133

AC:

AN:

754

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.000590

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.2

(source)

DANN

Benign

0.44

PhyloP100

-2.4

Mutation Taster

=100/0

polymorphism

(source)

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

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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