Genetic Variant ASMER1:n.87+62830A>G (chr21-14951514-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000432230.6(ASMER1):n.87+62830A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,154 control chromosomes in the GnomAD database, including 1,361 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 0.13 ( 1361 hom., cov: 32)

Consequence

ASMER1
ENST00000432230.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.698

Publications

4 publications found

Variant links:

Genes affected

ASMER1 (HGNC:53135): (adipocyte associated metabolic related lncRNA 1)

ASMER1 links:

Genome browser will be placed here

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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ASMER1	ENST00000432230.6 link	n.87+62830A>G	intron_variant	Intron 1 of 3	5
ASMER1	ENST00000715910.1 link	n.107+91981A>G	intron_variant	Intron 2 of 4
ASMER1	ENST00000850670.1 link	n.114-48518A>G	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19689

AN:

152036

Hom.:

1363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0795

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.0917

Gnomad EAS

AF:

0.172

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.127

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

GnomAD4 genome

AF:

0.130

AC:

19705

AN:

152154

Hom.:

1361

Cov.:

AF XY:

0.132

AC XY:

9832

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0796

AC:

3304

AN:

41524

American (AMR)

AF:

0.143

AC:

2191

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0917

AC:

318

AN:

3466

East Asian (EAS)

AF:

0.172

AC:

889

AN:

5170

South Asian (SAS)

AF:

0.195

AC:

942

AN:

4820

European-Finnish (FIN)

AF:

0.140

AC:

1486

AN:

10584

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10174

AN:

67998

Other (OTH)

AF:

0.127

AC:

269

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

881

1763

2644

3526

4407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.139

Hom.:

2168

Bravo

AF:

0.123

Asia WGS

AF:

0.184

AC:

639

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.2

(source)

DANN

Benign

0.72

PhyloP100

0.70

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over