dbSNP rs10106208: HAS2-AS1:n.310+25415G>A (chr8-121733090-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000647560.2(HAS2-AS1):n.310+25415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,192 control chromosomes in the GnomAD database, including 431 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 0.066 ( 431 hom., cov: 32)

Consequence

HAS2-AS1
ENST00000647560.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.900

Publications

0 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
HAS2-AS1	ENST00000647560.2 link	n.310+25415G>A	intron_variant	Intron 2 of 3
HAS2-AS1	ENST00000648171.1 link	n.884+25415G>A	intron_variant	Intron 6 of 8
HAS2-AS1	ENST00000653591.1 link	n.283+25415G>A	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.0658

AC:

10006

AN:

152074

Hom.:

431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0187

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.0547

Gnomad ASJ

AF:

0.0888

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0298

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0974

Gnomad OTH

AF:

0.0653

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

GnomAD4 genome

AF:

0.0657

AC:

10005

AN:

152192

Hom.:

431

Cov.:

AF XY:

0.0639

AC XY:

4754

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.0186

AC:

774

AN:

41536

American (AMR)

AF:

0.0547

AC:

837

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0888

AC:

308

AN:

3470

East Asian (EAS)

AF:

0.000771

AC:

AN:

5186

South Asian (SAS)

AF:

0.0298

AC:

144

AN:

4826

European-Finnish (FIN)

AF:

0.101

AC:

1068

AN:

10564

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0974

AC:

6626

AN:

68010

Other (OTH)

AF:

0.0646

AC:

136

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

492

984

1476

1968

2460

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0882

Hom.:

356

Bravo

AF:

0.0604

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.6

(source)

DANN

Benign

0.78

PhyloP100

-0.90

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