dbSNP rs1297214: ASMER1:n.87+54812C>A (chr21-14959532-G-T) – 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+54812C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,074 control chromosomes in the GnomAD database, including 2,322 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 0.16 ( 2322 hom., cov: 32)

Consequence

ASMER1
ENST00000432230.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.544

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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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+54812C>A	intron_variant	Intron 1 of 3	5
ASMER1	ENST00000715910.1 link	n.107+83963C>A	intron_variant	Intron 2 of 4
ASMER1	ENST00000850670.1 link	n.113+54812C>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24949

AN:

151956

Hom.:

2322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0952

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.177

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

GnomAD4 genome

AF:

0.164

AC:

24965

AN:

152074

Hom.:

2322

Cov.:

AF XY:

0.162

AC XY:

12018

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.0953

AC:

3955

AN:

41498

American (AMR)

AF:

0.130

AC:

1984

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

534

AN:

3466

East Asian (EAS)

AF:

0.142

AC:

732

AN:

5172

South Asian (SAS)

AF:

0.150

AC:

725

AN:

4824

European-Finnish (FIN)

AF:

0.207

AC:

2190

AN:

10568

Middle Eastern (MID)

AF:

0.250

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.208

AC:

14129

AN:

67954

Other (OTH)

AF:

0.176

AC:

371

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1046

2092

3139

4185

5231

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.193

Hom.:

5072

Bravo

AF:

0.156

Asia WGS

AF:

0.148

AC:

515

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.1

(source)

DANN

Benign

0.75

PhyloP100

-0.54

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