dbSNP rs12542166: ENSG00000254303:n.281+11018T>G (chr8-121970599-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000523792.1(ENSG00000254303):n.281+11018T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 152,242 control chromosomes in the GnomAD database, including 438 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 0.067 ( 438 hom., cov: 32)

Consequence

ENSG00000254303
ENST00000523792.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.704

Publications

1 publications found

Variant links:

Genes affected

ENSG00000254303 (HGNC:):

ENSG00000254303 links:

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=-0.69).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0947 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
ENSG00000254303	ENST00000523792.1 link	n.281+11018T>G	intron_variant	Intron 2 of 2	1
HAS2-AS1	ENST00000647560.2 link	n.447-22999A>C	intron_variant	Intron 3 of 3
HAS2-AS1	ENST00000653591.1 link	n.764-22999A>C	intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.0674

AC:

10254

AN:

152124

Hom.:

435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0168

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.0837

Gnomad ASJ

AF:

0.0484

Gnomad EAS

AF:

0.0588

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0861

Gnomad OTH

AF:

0.0622

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

GnomAD4 genome

AF:

0.0675

AC:

10274

AN:

152242

Hom.:

438

Cov.:

AF XY:

0.0685

AC XY:

5097

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0168

AC:

698

AN:

41572

American (AMR)

AF:

0.0841

AC:

1286

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0484

AC:

168

AN:

3470

East Asian (EAS)

AF:

0.0589

AC:

305

AN:

5178

South Asian (SAS)

AF:

0.102

AC:

493

AN:

4826

European-Finnish (FIN)

AF:

0.114

AC:

1208

AN:

10596

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0862

AC:

5859

AN:

67998

Other (OTH)

AF:

0.0653

AC:

138

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

489

978

1468

1957

2446

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0636

Hom.:

215

Bravo

AF:

0.0619

Asia WGS

AF:

0.0940

AC:

325

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

7.1

(source)

DANN

Benign

0.80

PhyloP100

0.70

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