dbSNP rs2248690: HRG-AS1:n.388+29655A>T (chr3-186612299-T-A) – 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+29655A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,172 control chromosomes in the GnomAD database, including 40,399 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 0.73 ( 40399 hom., cov: 33)

Consequence

HRG-AS1
ENST00000625386.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.116

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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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+29655A>T	intron_variant	Intron 3 of 3	5
HRG-AS1	ENST00000628505.2 link	n.390-5990A>T	intron_variant	Intron 3 of 3	5
HRG-AS1	ENST00000630178.2 link	n.239-32333A>T	intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.728

AC:

110632

AN:

152054

Hom.:

40378

Cov.:

show subpopulations

Gnomad AFR

AF:

0.718

Gnomad AMI

AF:

0.788

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.828

Gnomad EAS

AF:

0.831

Gnomad SAS

AF:

0.829

Gnomad FIN

AF:

0.649

Gnomad MID

AF:

0.918

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.765

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

GnomAD4 genome

AF:

0.727

AC:

110704

AN:

152172

Hom.:

40399

Cov.:

AF XY:

0.725

AC XY:

53948

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.718

Gnomad4 AMR

AF:

0.671

Gnomad4 ASJ

AF:

0.828

Gnomad4 EAS

AF:

0.830

Gnomad4 SAS

AF:

0.829

Gnomad4 FIN

AF:

0.649

Gnomad4 NFE

AF:

0.735

Gnomad4 OTH

AF:

0.763

Alfa

AF:

0.734

Hom.:

5138

Bravo

AF:

0.729

Asia WGS

AF:

0.800

AC:

2781

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

4.6

DANN

Benign

0.50

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