chr3-186622052-G-C

Position:

• chr3-186622052-G-C

Variant summary

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

The ENST00000630178.2(HRG-AS1):​n.239-42086C>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 0.185 in 152,056 control chromosomes in the GnomAD database, including 3,429 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 0.19 (3429 hom., cov: 32)
• Consequence: HRG-AS1 ENST00000630178.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HRG-AS1	ENST00000630178.2	n.239-42086C>G		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000625386.2	n.388+19902C>G		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000628505.2	n.390-15743C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28164 AN: 151938 Hom.: 3425 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.185 AC: 28176 AN: 152056 Hom.: 3429 Cov.: 32 AF XY: 0.182 AC XY: 13572 AN XY: 74368

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.192

Alfa AF: 0.137 Hom.: 257

Bravo AF: 0.196

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6787344; hg19: chr3-186339841;