rs1431087

Variant names:

• chr2-225619117-A-G
• rs1431087
• NM_001371273.1:c.1619-7800A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-225619117-A-G
• chr2-225619117-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NYAP2	NM_001371273.1	c.1619-7800A>G		intron_variant	Intron 5 of 7	ENST00000272907.8	NP_001358202.1
NYAP2	NM_020864.2	c.1619-7800A>G		intron_variant	Intron 4 of 5		NP_065915.1
NYAP2	XM_047445200.1	c.1619-7800A>G		intron_variant	Intron 5 of 7		XP_047301156.1
NYAP2	XM_047445201.1	c.1619-7800A>G		intron_variant	Intron 6 of 8		XP_047301157.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NYAP2	ENST00000272907.8	c.1619-7800A>G		intron_variant	Intron 5 of 7	1	NM_001371273.1	ENSP00000272907.7
NYAP2	ENST00000636099.1	c.1619-7800A>G		intron_variant	Intron 5 of 6	5		ENSP00000490942.1
NYAP2	ENST00000695959.1	c.128-7800A>G		intron_variant	Intron 1 of 3			ENSP00000512287.1

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

African (AFR) AF: 0.387 AC: 16065 AN: 41480

American (AMR) AF: 0.646 AC: 9876 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1965 AN: 3472

East Asian (EAS) AF: 0.503 AC: 2593 AN: 5160

South Asian (SAS) AF: 0.667 AC: 3215 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5401 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36780 AN: 67982

Other (OTH) AF: 0.549 AC: 1160 AN: 2112

Alfa AF: 0.491 Hom.: 5851

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
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1431087; hg19: chr2-226483833;