rs2880416

chr4-155203391-C-G

Variant summary

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

The XR_001741894.2(NPY2R-AS1):n.4573G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,032 control chromosomes in the GnomAD database, including 3,445 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 0.19 (3445 hom., cov: 33)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

NPY2R-AS1 (HGNC:):

MAP9-AS1 (HGNC:56110): (MAP9 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY2R-AS1	XR_001741894.2	n.4573G>C		non_coding_transcript_exon_variant	2/2
NPY2R	NM_001375470.1	c.-48-10501C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP9-AS1	ENST00000630664.2	n.208+29107C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28858 AN: 151914 Hom.: 3446 Cov.: 33

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.190 AC: 28847 AN: 152032 Hom.: 3445 Cov.: 33 AF XY: 0.203 AC XY: 15053 AN XY: 74290

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.193

Alfa AF: 0.201 Hom.: 433

Bravo AF: 0.178

Asia WGS AF: 0.385 AC: 1335 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.39
Dann	Benign	0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2880416; hg19: chr4-156124543;