rs12507396

chr4-155207892-A-T

Variant summary

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

The ENST00000511017.6(NPY2R-AS1):n.329-77T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,222 control chromosomes in the GnomAD database, including 983 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 0.10 (982 hom., cov: 33)
  • Exomes 𝑓: 0.16 (1 hom.)
• Consequence: NPY2R-AS1 ENST00000511017.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

Genes affected

NPY2R-AS1 (HGNC:55549): (NPY2R antisense RNA 1)

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

NPY2R (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY2R-AS1	XR_001741894.2	n.149-77T>A		intron_variant, non_coding_transcript_variant
NPY2R	NM_001375470.1	c.-48-6000A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPY2R-AS1	ENST00000511017.6	n.329-77T>A		intron_variant, non_coding_transcript_variant		3
MAP9-AS1	ENST00000630664.2	n.208+33608A>T		intron_variant, non_coding_transcript_variant		5
NPY2R-AS1	ENST00000508687.1	n.219-77T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15872 AN: 152022 Hom.: 979 Cov.: 33

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.101

GnomAD4 exome AF: 0.159 AC: 13 AN: 82 Hom.: 1 Cov.: 0 AF XY: 0.172 AC XY: 10 AN XY: 58

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.104 AC: 15874 AN: 152140 Hom.: 982 Cov.: 33 AF XY: 0.107 AC XY: 7973 AN XY: 74380

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0998

Alfa AF: 0.117 Hom.: 151

Bravo AF: 0.102

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.0
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12507396; hg19: chr4-156129044;