16-29383501-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001310137.5(NPIPB11):ā€‹c.1431T>Cā€‹(p.Ser477=) 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 (ā˜…).

Frequency

Genomes: š‘“ 0.00038 ( 0 hom., cov: 9)
Exomes š‘“: 0.0012 ( 232 hom. )
Failed GnomAD Quality Control

Consequence

NPIPB11
NM_001310137.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.47
Variant links:
Genes affected
NPIPB11 (HGNC:37453): (nuclear pore complex interacting protein family member B11) Predicted to act upstream of or within prevention of polyspermy. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.07).
BP6
Variant 16-29383501-A-G is Benign according to our data. Variant chr16-29383501-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2646361.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.47 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NPIPB11NM_001310137.5 linkuse as main transcriptc.1431T>C p.Ser477= synonymous_variant 8/8 ENST00000698511.1 NP_001297066.2
NPIPB11XM_047434576.1 linkuse as main transcriptc.1431T>C p.Ser477= synonymous_variant 7/8 XP_047290532.1
NPIPB11XM_047434577.1 linkuse as main transcriptc.1086-21T>C intron_variant XP_047290533.1
NPIPB11XM_047434578.1 linkuse as main transcriptc.1029-21T>C intron_variant XP_047290534.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NPIPB11ENST00000698511.1 linkuse as main transcriptc.1431T>C p.Ser477= synonymous_variant 8/8 NM_001310137.5 ENSP00000513761 P1
NPIPB11ENST00000524087.5 linkuse as main transcriptc.1431T>C p.Ser477= synonymous_variant 8/85 ENSP00000430853 P1

Frequencies

GnomAD3 genomes
AF:
0.000384
AC:
25
AN:
65060
Hom.:
0
Cov.:
9
show subpopulations
Gnomad AFR
AF:
0.000119
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000179
Gnomad ASJ
AF:
0.000566
Gnomad EAS
AF:
0.00364
Gnomad SAS
AF:
0.000906
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000494
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00235
AC:
453
AN:
192582
Hom.:
58
AF XY:
0.00220
AC XY:
234
AN XY:
106222
show subpopulations
Gnomad AFR exome
AF:
0.000998
Gnomad AMR exome
AF:
0.00348
Gnomad ASJ exome
AF:
0.00440
Gnomad EAS exome
AF:
0.00229
Gnomad SAS exome
AF:
0.00139
Gnomad FIN exome
AF:
0.00130
Gnomad NFE exome
AF:
0.00226
Gnomad OTH exome
AF:
0.00580
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00117
AC:
1389
AN:
1186790
Hom.:
232
Cov.:
34
AF XY:
0.00127
AC XY:
753
AN XY:
592172
show subpopulations
Gnomad4 AFR exome
AF:
0.000391
Gnomad4 AMR exome
AF:
0.00167
Gnomad4 ASJ exome
AF:
0.00344
Gnomad4 EAS exome
AF:
0.000677
Gnomad4 SAS exome
AF:
0.00250
Gnomad4 FIN exome
AF:
0.00316
Gnomad4 NFE exome
AF:
0.000941
Gnomad4 OTH exome
AF:
0.00149
GnomAD4 genome
AF:
0.000384
AC:
25
AN:
65098
Hom.:
0
Cov.:
9
AF XY:
0.000425
AC XY:
13
AN XY:
30590
show subpopulations
Gnomad4 AFR
AF:
0.000118
Gnomad4 AMR
AF:
0.000179
Gnomad4 ASJ
AF:
0.000566
Gnomad4 EAS
AF:
0.00365
Gnomad4 SAS
AF:
0.000916
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000494
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2023NPIPB11: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
3.8
DANN
Benign
0.27

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.

Other links and lift over

dbSNP: rs376240593; hg19: chr16-29394822; COSMIC: COSV105936522; COSMIC: COSV105936522; API