Genetic Variant HRG-AS1:n.651-771A>G (chr3-186715310-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000354642.4(HRG-AS1):n.651-771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,664 control chromosomes in the GnomAD database, including 10,032 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 0.36 ( 10032 hom., cov: 30)

Consequence

HRG-AS1
ENST00000354642.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.439

Publications

28 publications found

Variant links:

COSMIC-nc: COSV107286310

Genes affected

HRG-AS1 (HGNC:55915): (HRG and FETUB antisense RNA 1)

HRG-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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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
HRG-AS1	ENST00000354642.4 link	n.651-771A>G	intron_variant	Intron 6 of 6	5
HRG-AS1	ENST00000625303.2 link	n.214+3157A>G	intron_variant	Intron 2 of 6	5
HRG-AS1	ENST00000625386.2 link	n.213+3157A>G	intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

53886

AN:

151544

Hom.:

10022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.458

Gnomad AMI

AF:

0.446

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.319

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

GnomAD4 genome

AF:

0.356

AC:

53938

AN:

151664

Hom.:

10032

Cov.:

AF XY:

0.353

AC XY:

26135

AN XY:

74136

show subpopulations

African (AFR)

AF:

0.458

AC:

18919

AN:

41290

American (AMR)

AF:

0.286

AC:

4368

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

954

AN:

3466

East Asian (EAS)

AF:

0.320

AC:

1641

AN:

5128

South Asian (SAS)

AF:

0.432

AC:

2081

AN:

4816

European-Finnish (FIN)

AF:

0.304

AC:

3207

AN:

10546

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.318

AC:

21596

AN:

67854

Other (OTH)

AF:

0.320

AC:

675

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1727

3454

5181

6908

8635

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.325

Hom.:

20163

Bravo

AF:

0.355

Asia WGS

AF:

0.391

AC:

1359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.3

(source)

DANN

Benign

0.36

PhyloP100

-0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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