dbSNP rs6787344: HRG-AS1:n.388+19902C>G (chr3-186622052-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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

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

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.152

Gnomad4 ASJ

AF:

0.189

Gnomad4 EAS

AF:

0.122

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.0914

Gnomad4 NFE

AF:

0.117

Gnomad4 OTH

AF:

0.192

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

DANN

Benign

0.55

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over