Genetic Variant HRG-AS1:n.388+19902C>G (chr3-186622052-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 ENST00000625386.2(HRG-AS1):n.388+19902C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,056 control chromosomes in the GnomAD database, including 3,429 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 0.19 ( 3429 hom., cov: 32)

Consequence

HRG-AS1
ENST00000625386.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158

Publications

4 publications found

Variant links:

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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	ENST00000625386.2 link	n.388+19902C>G	intron_variant	Intron 3 of 3	5
HRG-AS1	ENST00000628505.2 link	n.390-15743C>G	intron_variant	Intron 3 of 3	5
HRG-AS1	ENST00000630178.2 link	n.239-42086C>G	intron_variant	Intron 2 of 2	5
HRG-AS1	ENST00000840331.1 link	n.174+13467C>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28164

AN:

151938

Hom.:

3425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.189

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.0914

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.192

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

GnomAD4 genome

AF:

0.185

AC:

28176

AN:

152056

Hom.:

3429

Cov.:

AF XY:

0.182

AC XY:

13572

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.342

AC:

14153

AN:

41420

American (AMR)

AF:

0.152

AC:

2332

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.189

AC:

655

AN:

3472

East Asian (EAS)

AF:

0.122

AC:

634

AN:

5184

South Asian (SAS)

AF:

0.199

AC:

958

AN:

4812

European-Finnish (FIN)

AF:

0.0914

AC:

968

AN:

10586

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7952

AN:

67976

Other (OTH)

AF:

0.192

AC:

404

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1049

2098

3146

4195

5244

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.137

Hom.:

257

Bravo

AF:

0.196

Asia WGS

AF:

0.176

AC:

613

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.8

(source)

DANN

Benign

0.55

PhyloP100

0.16

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