3-186612299-T-A

Variant names:

• chr3-186612299-T-A
• rs2248690
• ENST00000625386.2:n.388+29655A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 41 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625386.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HRG-AS1	ENST00000625386.2	TSL:5	n.388+29655A>T		intron	N/A
	HRG-AS1	ENST00000628505.2	TSL:5	n.390-5990A>T		intron	N/A
	HRG-AS1	ENST00000630178.2	TSL:5	n.239-32333A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110632 AN: 152054 Hom.: 40378 Cov.: 33

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.: 33 AF XY: 0.725 AC XY: 53948 AN XY: 74384

African (AFR) AF: 0.718 AC: 29824 AN: 41526

American (AMR) AF: 0.671 AC: 10256 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2870 AN: 3468

East Asian (EAS) AF: 0.830 AC: 4293 AN: 5172

South Asian (SAS) AF: 0.829 AC: 3999 AN: 4824

European-Finnish (FIN) AF: 0.649 AC: 6870 AN: 10586

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49994 AN: 67990

Other (OTH) AF: 0.763 AC: 1613 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.50
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2248690; hg19: chr3-186330088;