rs1431087

chr2-225619117-A-Gchr2-225619117-A-T

Variant summary

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

The NM_001371273.1(NYAP2):c.1619-7800A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,068 control chromosomes in the GnomAD database, including 20,468 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 0.51 (20468 hom., cov: 32)
• Consequence: NYAP2 NM_001371273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

NYAP2 (HGNC:29291): (neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2) Predicted to be involved in neuron projection morphogenesis and phosphatidylinositol 3-kinase signaling. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NYAP2	NM_001371273.1	c.1619-7800A>G		intron_variant		ENST00000272907.8
NYAP2	NM_020864.2	c.1619-7800A>G		intron_variant
NYAP2	XM_047445200.1	c.1619-7800A>G		intron_variant
NYAP2	XM_047445201.1	c.1619-7800A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NYAP2	ENST00000272907.8	c.1619-7800A>G		intron_variant		1	NM_001371273.1	P1
NYAP2	ENST00000636099.1	c.1619-7800A>G		intron_variant		5
NYAP2	ENST00000695959.1	c.129-7800A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77705 AN: 151950 Hom.: 20445 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.511 AC: 77772 AN: 152068 Hom.: 20468 Cov.: 32 AF XY: 0.516 AC XY: 38327 AN XY: 74328

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.549

Alfa AF: 0.480 Hom.: 4239

Bravo AF: 0.514

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.27
Dann	Benign	0.81

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: rs1431087; hg19: chr2-226483833;