rs528769988

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014697.3(NOS1AP):​c.-273C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 184,708 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 78 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 1 hom. )

Consequence

NOS1AP
NM_014697.3 5_prime_UTR

Scores

1
1

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0130
Variant links:
Genes affected
NOS1AP (HGNC:16859): (nitric oxide synthase 1 adaptor protein) This gene encodes a cytosolic protein that binds to the signaling molecule, neuronal nitric oxide synthase (nNOS). This protein has a C-terminal PDZ-binding domain that mediates interactions with nNOS and an N-terminal phosphotyrosine binding (PTB) domain that binds to the small monomeric G protein, Dexras1. Studies of the related mouse and rat proteins have shown that this protein functions as an adapter protein linking nNOS to specific targets, such as Dexras1 and the synapsins. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 1-162069905-C-T is Benign according to our data. Variant chr1-162069905-C-T is described in ClinVar as [Benign]. Clinvar id is 1276155.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0552 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NOS1APNM_014697.3 linkc.-273C>T 5_prime_UTR_variant Exon 1 of 10 ENST00000361897.10 NP_055512.1 O75052-1
NOS1APNM_001164757.2 linkc.-273C>T 5_prime_UTR_variant Exon 1 of 10 NP_001158229.1 O75052-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NOS1APENST00000361897 linkc.-273C>T 5_prime_UTR_variant Exon 1 of 10 1 NM_014697.3 ENSP00000355133.5 O75052-1
NOS1APENST00000530878 linkc.-273C>T 5_prime_UTR_variant Exon 1 of 10 1 ENSP00000431586.1 O75052-3

Frequencies

GnomAD3 genomes
AF:
0.0162
AC:
2460
AN:
151628
Hom.:
77
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0572
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00322
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000309
Gnomad OTH
AF:
0.0120
GnomAD4 exome
AF:
0.00212
AC:
70
AN:
32972
Hom.:
1
Cov.:
0
AF XY:
0.00158
AC XY:
28
AN XY:
17768
show subpopulations
Gnomad4 AFR exome
AF:
0.0554
Gnomad4 AMR exome
AF:
0.00130
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000327
Gnomad4 NFE exome
AF:
0.000452
Gnomad4 OTH exome
AF:
0.00400
GnomAD4 genome
AF:
0.0162
AC:
2463
AN:
151736
Hom.:
78
Cov.:
33
AF XY:
0.0156
AC XY:
1155
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.0571
Gnomad4 AMR
AF:
0.00321
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000309
Gnomad4 OTH
AF:
0.0119
Alfa
AF:
0.0101
Hom.:
5
Bravo
AF:
0.0181
Asia WGS
AF:
0.00236
AC:
8
AN:
3410

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
May 15, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
14
DANN
Uncertain
0.98

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: rs528769988; hg19: chr1-162039695; API