rs2077119

chr3-186612673-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000630178.2(HRG-AS1):n.239-32707A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,100 control chromosomes in the GnomAD database, including 11,284 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 0.35 (11284 hom., cov: 31)
• Consequence: HRG-AS1 ENST00000630178.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HRG-AS1	ENST00000630178.2	n.239-32707A>C		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000625386.2	n.388+29281A>C		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000628505.2	n.390-6364A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52922 AN: 151982 Hom.: 11283 Cov.: 31

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.348 AC: 52934 AN: 152100 Hom.: 11284 Cov.: 31 AF XY: 0.350 AC XY: 26019 AN XY: 74328

Gnomad4 AFR AF: 0.0937

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.392

Alfa AF: 0.438 Hom.: 14066

Bravo AF: 0.340

Asia WGS AF: 0.492 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.44
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077119; hg19: chr3-186330462;