dbSNP rs10482862: 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

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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