4-155208030-C-T

Position:

• chr4-155208030-C-T

Variant summary

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

The ENST00000511017.6(NPY2R-AS1):​n.323G>A 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 0.493 in 152,184 control chromosomes in the GnomAD database, including 20,038 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 0.49 (20027 hom., cov: 32)
  • Exomes 𝑓: 0.35 (11 hom.)
• Consequence: NPY2R-AS1 ENST00000511017.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.69

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY2R-AS1	XR_001741894.2	n.143G>A		non_coding_transcript_exon_variant	1/2
NPY2R	NM_001375470.1	c.-48-5862C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPY2R-AS1	ENST00000511017.6	n.323G>A		non_coding_transcript_exon_variant	2/3	3
MAP9-AS1	ENST00000630664.2	n.208+33746C>T		intron_variant, non_coding_transcript_variant		5
NPY2R-AS1	ENST00000508687.1	n.213G>A		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74811 AN: 151898 Hom.: 19981 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.463

GnomAD4 exome AF: 0.351 AC: 59 AN: 168 Hom.: 11 Cov.: 0 AF XY: 0.344 AC XY: 44 AN XY: 128

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.356

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.493 AC: 74921 AN: 152016 Hom.: 20027 Cov.: 32 AF XY: 0.493 AC XY: 36652 AN XY: 74326

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.468

Alfa AF: 0.385 Hom.: 7531

Bravo AF: 0.497

Asia WGS AF: 0.472 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.39
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6857715; hg19: chr4-156129182;