rs2880412

chr4-155190827-A-C

Variant summary

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

The ENST00000630664.2(MAP9-AS1):n.208+16543A>C 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 0.255 in 151,776 control chromosomes in the GnomAD database, including 5,716 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 0.26 (5716 hom., cov: 32)
• Consequence: MAP9-AS1 ENST00000630664.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY2R	NM_001375470.1	c.-49+17031A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP9-AS1	ENST00000630664.2	n.208+16543A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38720 AN: 151658 Hom.: 5700 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.255 AC: 38766 AN: 151776 Hom.: 5716 Cov.: 32 AF XY: 0.261 AC XY: 19390 AN XY: 74180

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.255

Alfa AF: 0.262 Hom.: 690

Bravo AF: 0.242

Asia WGS AF: 0.423 AC: 1468 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
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: rs2880412; hg19: chr4-156111979;