3-186715310-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.238+3157A>G 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 0.356 in 151,664 control chromosomes in the GnomAD database, including 10,032 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 0.36 (10032 hom., cov: 30)
• Consequence: HRG-AS1 ENST00000630178.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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.238+3157A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53886 AN: 151544 Hom.: 10022 Cov.: 30

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.356 AC: 53938 AN: 151664 Hom.: 10032 Cov.: 30 AF XY: 0.353 AC XY: 26135 AN XY: 74136

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.320

Alfa AF: 0.305 Hom.: 5051

Bravo AF: 0.355

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.3
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11924390; hg19: chr3-186433099;