chr1-162115895-G-T

Position:

• chr1-162115895-G-T

Variant summary

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

The NM_014697.3(NOS1AP):​c.106-38510G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,000 control chromosomes in the GnomAD database, including 23,424 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 0.54 (23424 hom., cov: 31)
• Consequence: NOS1AP NM_014697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOS1AP	NM_014697.3	c.106-38510G>T		intron_variant		ENST00000361897.10
LOC105371475	XR_007066699.1	n.487-1993C>A		intron_variant, non_coding_transcript_variant
NOS1AP	NM_001164757.2	c.106-38510G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOS1AP	ENST00000361897.10	c.106-38510G>T		intron_variant		1	NM_014697.3
NOS1AP	ENST00000530878.5	c.106-38510G>T		intron_variant		1		P1
NOS1AP	ENST00000430120.3	c.106-38510G>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82143 AN: 151882 Hom.: 23407 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.541 AC: 82191 AN: 152000 Hom.: 23424 Cov.: 31 AF XY: 0.539 AC XY: 40068 AN XY: 74306

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.555

Alfa AF: 0.614 Hom.: 50887

Bravo AF: 0.538

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.67

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: rs10494366; hg19: chr1-162085685;