dbSNP rs12602486: ASB16-AS1:n.186-7102A>C (chr17-44164561-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000755665.1(ASB16-AS1):n.186-7102A>C variant causes a intron change. The variant allele was found at a frequency of 0.0377 in 152,268 control chromosomes in the GnomAD database, including 139 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 0.038 ( 139 hom., cov: 31)

Consequence

ASB16-AS1
ENST00000755665.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned

Publications

10 publications found

Variant links:

Genes affected

ASB16-AS1 (HGNC:25442): (ASB16 antisense RNA 1)

ASB16-AS1 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB16-AS1	ENST00000755665.1 link	n.186-7102A>C		intron_variant	Intron 1 of 1
ASB16-AS1	ENST00000755666.1 link	n.236-4855A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0377

AC:

5742

AN:

152150

Hom.:

138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0370

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0509

Gnomad ASJ

AF:

0.0666

Gnomad EAS

AF:

0.0684

Gnomad SAS

AF:

0.0323

Gnomad FIN

AF:

0.0241

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0341

Gnomad OTH

AF:

0.0325

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

GnomAD4 genome

AF:

0.0377

AC:

5747

AN:

152268

Hom.:

139

Cov.:

AF XY:

0.0373

AC XY:

2780

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0370

AC:

1537

AN:

41568

American (AMR)

AF:

0.0509

AC:

778

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0666

AC:

231

AN:

3470

East Asian (EAS)

AF:

0.0686

AC:

355

AN:

5178

South Asian (SAS)

AF:

0.0329

AC:

159

AN:

4826

European-Finnish (FIN)

AF:

0.0241

AC:

256

AN:

10616

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0341

AC:

2322

AN:

68018

Other (OTH)

AF:

0.0317

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

275

550

824

1099

1374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0409

Hom.:

Bravo

AF:

0.0413

Asia WGS

AF:

0.0550

AC:

192

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.48

(source)

DANN

Benign

0.31

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