Genetic Variant ENST00000596329.3:n.515-1643C>T (chr3-186748463-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 ENST00000596329.3(HRG-AS1):n.515-1643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,992 control chromosomes in the GnomAD database, including 2,550 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 0.18 ( 2550 hom., cov: 31)

Consequence

HRG-AS1
ENST00000596329.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

Publications

16 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=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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	ENST00000596329.3 link	n.515-1643C>T	intron_variant	Intron 1 of 2	5
HRG-AS1	ENST00000596632.1 link	n.432-3261C>T	intron_variant	Intron 1 of 2	5
HRG-AS1	ENST00000599314.5 link	n.61-4622C>T	intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27287

AN:

151874

Hom.:

2552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.152

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

GnomAD4 genome

AF:

0.180

AC:

27300

AN:

151992

Hom.:

2550

Cov.:

AF XY:

0.181

AC XY:

13461

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.200

AC:

8311

AN:

41470

American (AMR)

AF:

0.138

AC:

2094

AN:

15220

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

455

AN:

3462

East Asian (EAS)

AF:

0.281

AC:

1451

AN:

5164

South Asian (SAS)

AF:

0.149

AC:

719

AN:

4822

European-Finnish (FIN)

AF:

0.192

AC:

2025

AN:

10562

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.173

AC:

11769

AN:

67978

Other (OTH)

AF:

0.151

AC:

319

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1097

2194

3290

4387

5484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<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:

0.174

Hom.:

9963

Bravo

AF:

0.176

Asia WGS

AF:

0.192

AC:

666

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

0.25

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