rs6849115

Positions:

• chr4-155203071-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001741894.2(NPY2R-AS1):​n.4893A>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 0.238 in 152,018 control chromosomes in the GnomAD database, including 4,645 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 0.24 (4645 hom., cov: 33)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

NPY2R-AS1 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.4893A>G		non_coding_transcript_exon_variant	2/2
NPY2R	NM_001375470.1	c.-48-10821T>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+28787T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36141 AN: 151900 Hom.: 4647 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.238 AC: 36140 AN: 152018 Hom.: 4645 Cov.: 33 AF XY: 0.248 AC XY: 18454 AN XY: 74296

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.232

Alfa AF: 0.207 Hom.: 5306

Bravo AF: 0.233

Asia WGS AF: 0.393 AC: 1361 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	16
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6849115; hg19: chr4-156124223;