dbSNP rs17304901: MAP9-AS1:n.399+42936G>A (chr4-155217220-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000630664.3(MAP9-AS1):n.399+42936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,612 control chromosomes in the GnomAD database, including 3,587 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 0.19 ( 3577 hom., cov: 32)

Exomes 𝑓: 0.19 ( 10 hom. )

Consequence

MAP9-AS1
ENST00000630664.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.821

Publications

9 publications found

Variant links:

Genes affected

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

MAP9-AS1 links:

NPY2R (HGNC:7957): (neuropeptide Y receptor Y2) Predicted to enable calcium channel regulator activity and neuropeptide Y receptor activity. Involved in cardiac left ventricle morphogenesis and outflow tract morphogenesis. Located in cilium. Implicated in Huntington's disease; morbid obesity; and obesity. Biomarker of peripheral artery disease and temporal lobe epilepsy. [provided by Alliance of Genome Resources, Apr 2022]

NPY2R links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630664.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NPY2R	NM_000910.4	MANE Select	c.*2135G>A	downstream_gene	N/A	NP_000901.1
NPY2R	NM_001370180.1		c.*2135G>A	downstream_gene	N/A	NP_001357109.1
NPY2R	NM_001375470.1		c.*2135G>A	downstream_gene	N/A	NP_001362399.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MAP9-AS1	ENST00000630664.3	TSL:5	n.399+42936G>A	intron	N/A
NPY2R	ENST00000329476.4	TSL:1 MANE Select	c.*2135G>A	downstream_gene	N/A	ENSP00000332591.3
NPY2R	ENST00000506608.1	TSL:1	c.*2135G>A	downstream_gene	N/A	ENSP00000426366.1

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29330

AN:

151960

Hom.:

3575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0609

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.0533

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.233

GnomAD4 exome

AF:

0.191

AC:

102

AN:

534

Hom.:

AF XY:

0.195

AC XY:

AN XY:

338

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.188

AC:

AN:

520

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.125

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.193

AC:

29335

AN:

152078

Hom.:

3577

Cov.:

AF XY:

0.191

AC XY:

14229

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0607

AC:

2521

AN:

41534

American (AMR)

AF:

0.232

AC:

3540

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.307

AC:

1063

AN:

3466

East Asian (EAS)

AF:

0.0539

AC:

278

AN:

5162

South Asian (SAS)

AF:

0.195

AC:

939

AN:

4822

European-Finnish (FIN)

AF:

0.202

AC:

2137

AN:

10568

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.266

AC:

18098

AN:

67946

Other (OTH)

AF:

0.230

AC:

485

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1160

2320

3481

4641

5801

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.244

Hom.:

9060

Bravo

AF:

0.192

Asia WGS

AF:

0.118

AC:

410

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.33

(source)

DANN

Benign

0.76

PhyloP100

-0.82

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over