rs12649641

Positions:

• chr4-155204181-C-A
• chr4-155204181-C-T

Variant summary

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

The XR_001741894.2(NPY2R-AS1):​n.3783G>T 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 151,246 control chromosomes in the GnomAD database, including 17,984 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 (17984 hom., cov: 30)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.3783G>T		non_coding_transcript_exon_variant	2/2
NPY2R	NM_001375470.1	c.-48-9711C>A		intron_variant			NP_001362399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP9-AS1	ENST00000630664.2	n.208+29897C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71637 AN: 151132 Hom.: 17944 Cov.: 30

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.474 AC: 71740 AN: 151246 Hom.: 17984 Cov.: 30 AF XY: 0.476 AC XY: 35117 AN XY: 73842

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.456

Alfa AF: 0.382 Hom.: 8523

Bravo AF: 0.477

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12649641; hg19: chr4-156125333;