4-155206115-T-C

Position:

• chr4-155206115-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.1849A>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 0.496 in 151,952 control chromosomes in the GnomAD database, including 20,245 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 0.50 (20245 hom., cov: 32)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.1849A>G		non_coding_transcript_exon_variant	2/2
NPY2R	NM_001375470.1	c.-48-7777T>C		intron_variant			NP_001362399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP9-AS1	ENST00000630664.2	n.208+31831T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75295 AN: 151834 Hom.: 20199 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.496 AC: 75405 AN: 151952 Hom.: 20245 Cov.: 32 AF XY: 0.496 AC XY: 36823 AN XY: 74242

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.473

Alfa AF: 0.419 Hom.: 5484

Bravo AF: 0.502

Asia WGS AF: 0.473 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.27
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10212868; hg19: chr4-156127267;