chr3-186762417-A-G

Variant names:

• chr3-186762417-A-G
• rs822354

Variant summary

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

The variant allele was found at a frequency of 0.718 in 152,162 control chromosomes in the GnomAD database, including 39,721 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 0.72 (39721 hom., cov: 33)
• Consequence: PSMD10P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 26 publications found

Genes affected

PSMD10P2 (HGNC:30151): (proteasome 26S subunit, non-ATPase, 10 pseudogene 2)

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625710.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HRG-AS1	ENST00000625710.3	TSL:5	n.144+10426T>C		intron	N/A
	HRG-AS1	ENST00000625869.1	TSL:5	n.144+10426T>C		intron	N/A
	HRG-AS1	ENST00000626520.2	TSL:5	n.121+10426T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109231 AN: 152044 Hom.: 39684 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.718 AC: 109324 AN: 152162 Hom.: 39721 Cov.: 33 AF XY: 0.719 AC XY: 53515 AN XY: 74390

African (AFR) AF: 0.796 AC: 33046 AN: 41524

American (AMR) AF: 0.615 AC: 9396 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2055 AN: 3472

East Asian (EAS) AF: 0.829 AC: 4293 AN: 5180

South Asian (SAS) AF: 0.800 AC: 3855 AN: 4820

European-Finnish (FIN) AF: 0.774 AC: 8193 AN: 10592

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46245 AN: 67978

Other (OTH) AF: 0.680 AC: 1436 AN: 2112

Alfa AF: 0.694 Hom.: 115534

Bravo AF: 0.709

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs822354; hg19: chr3-186480206;