rs2248690

chr3-186612299-T-Achr3-186612299-T-C

Variant summary

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

The ENST00000630178.2(HRG-AS1):n.239-32333A>T 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 0.727 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 ENST00000630178.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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=-0.78).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HRG-AS1	ENST00000630178.2	n.239-32333A>T		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000625386.2	n.388+29655A>T		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000628505.2	n.390-5990A>T		intron_variant, non_coding_transcript_variant		5

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

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

Other links and lift over

dbSNP: rs2248690; hg19: chr3-186330088;