dbSNP rs956225: HAS2-AS1:n.315-5991A>G (chr8-121897448-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000523550.1(HAS2-AS1):n.315-5991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,150 control chromosomes in the GnomAD database, including 1,325 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 0.12 ( 1325 hom., cov: 32)

Consequence

HAS2-AS1
ENST00000523550.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.715

Publications

10 publications found

Variant links:

Genes affected

HAS2-AS1 (HGNC:34340): (HAS2 antisense RNA 1)

HAS2-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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 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
HAS2-AS1	ENST00000523550.1 link	n.315-5991A>G	intron_variant	Intron 2 of 3	3
HAS2-AS1	ENST00000647560.2 link	n.446+17683A>G	intron_variant	Intron 3 of 3
HAS2-AS1	ENST00000648171.1 link	n.969-5991A>G	intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18108

AN:

152032

Hom.:

1325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0287

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.130

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

GnomAD4 genome

AF:

0.119

AC:

18104

AN:

152150

Hom.:

1325

Cov.:

AF XY:

0.122

AC XY:

9107

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0286

AC:

1189

AN:

41546

American (AMR)

AF:

0.114

AC:

1751

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

540

AN:

3468

East Asian (EAS)

AF:

0.131

AC:

676

AN:

5174

South Asian (SAS)

AF:

0.120

AC:

580

AN:

4828

European-Finnish (FIN)

AF:

0.221

AC:

2334

AN:

10556

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.156

AC:

10583

AN:

67964

Other (OTH)

AF:

0.132

AC:

278

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

810

1621

2431

3242

4052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.140

Hom.:

5564

Bravo

AF:

0.109

Asia WGS

AF:

0.129

AC:

448

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.21

(source)

DANN

Benign

0.48

PhyloP100

-0.71

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