chr1-162129511-G-A

Position:

• chr1-162129511-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014697.3(NOS1AP):​c.106-24894G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,088 control chromosomes in the GnomAD database, including 8,083 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (8083 hom., cov: 32)
• Consequence: NOS1AP NM_014697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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]

LOC105371475 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOS1AP	NM_014697.3	c.106-24894G>A		intron_variant		ENST00000361897.10
LOC105371475	XR_007066699.1	n.487-15609C>T		intron_variant, non_coding_transcript_variant
NOS1AP	NM_001164757.2	c.106-24894G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOS1AP	ENST00000361897.10	c.106-24894G>A		intron_variant		1	NM_014697.3
NOS1AP	ENST00000530878.5	c.106-24894G>A		intron_variant		1		P1
NOS1AP	ENST00000430120.3	c.106-24894G>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35574 AN: 151970 Hom.: 8065 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.190

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.234 AC: 35635 AN: 152088 Hom.: 8083 Cov.: 32 AF XY: 0.228 AC XY: 16949 AN XY: 74346

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.0734

Gnomad4 FIN AF: 0.0774

Gnomad4 NFE AF: 0.0909

Gnomad4 OTH AF: 0.188

Alfa AF: 0.0992 Hom.: 2475

Bravo AF: 0.253

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.80

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

Other links and lift over

dbSNP: rs1572495; hg19: chr1-162099301;