dbSNP rs6981419: HAS2-AS1:n.311-809G>C (chr8-121878821-G-C) – 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.311-809G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 152,004 control chromosomes in the GnomAD database, including 122 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 0.026 ( 122 hom., cov: 32)

Consequence

HAS2-AS1
ENST00000647560.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.316

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 (AFR) 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	Effect	Exon rank
HAS2-AS1	ENST00000647560.2 link	n.311-809G>C	intron_variant	Intron 2 of 3
HAS2-AS1	ENST00000648171.1 link	n.968+15812G>C	intron_variant	Intron 7 of 8
HAS2-AS1	ENST00000653591.1 link	n.368-809G>C	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.0262

AC:

3972

AN:

151886

Hom.:

121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0645

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0418

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0601

Gnomad SAS

AF:

0.0363

Gnomad FIN

AF:

0.00588

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000794

Gnomad OTH

AF:

0.0297

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

GnomAD4 genome

AF:

0.0262

AC:

3990

AN:

152004

Hom.:

122

Cov.:

AF XY:

0.0265

AC XY:

1969

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.0648

AC:

2684

AN:

41444

American (AMR)

AF:

0.0418

AC:

638

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.0598

AC:

309

AN:

5166

South Asian (SAS)

AF:

0.0359

AC:

173

AN:

4814

European-Finnish (FIN)

AF:

0.00588

AC:

AN:

10548

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000794

AC:

AN:

67968

Other (OTH)

AF:

0.0313

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

184

369

553

738

922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

176

220

<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:

0.00114

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

(source)

DANN

Benign

0.65

PhyloP100

0.32

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