rs12641982

chr4-155202442-A-Gchr4-155202442-A-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.5522T>C 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 0.714 in 152,074 control chromosomes in the GnomAD database, including 40,339 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 0.71 (40339 hom., cov: 32)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY2R-AS1	XR_001741894.2	n.5522T>C		non_coding_transcript_exon_variant	2/2
NPY2R	NM_001375470.1	c.-48-11450A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP9-AS1	ENST00000630664.2	n.208+28158A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108403 AN: 151956 Hom.: 40290 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.714 AC: 108514 AN: 152074 Hom.: 40339 Cov.: 32 AF XY: 0.725 AC XY: 53946 AN XY: 74368

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.691

Alfa AF: 0.676 Hom.: 4909

Bravo AF: 0.711

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.9
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12641982; hg19: chr4-156123594;