rs2342676

chr4-155203552-T-C

Variant summary

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

The XR_001741894.2(NPY2R-AS1):n.4412A>G 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 0.474 in 151,748 control chromosomes in the GnomAD database, including 17,981 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 0.47 (17981 hom., cov: 32)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY2R-AS1	XR_001741894.2	n.4412A>G		non_coding_transcript_exon_variant	2/2
NPY2R	NM_001375470.1	c.-48-10340T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP9-AS1	ENST00000630664.2	n.208+29268T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71784 AN: 151632 Hom.: 17943 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.474 AC: 71886 AN: 151748 Hom.: 17981 Cov.: 32 AF XY: 0.475 AC XY: 35186 AN XY: 74150

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.458

Alfa AF: 0.428 Hom.: 1846

Bravo AF: 0.477

Asia WGS AF: 0.470 AC: 1636 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.0
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2342676; hg19: chr4-156124704;