3-186762417-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMD10P2		n.186762417A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HRG-AS1	ENST00000625710.3	n.144+10426T>C		intron_variant	Intron 1 of 2	5
HRG-AS1	ENST00000625869.1	n.144+10426T>C		intron_variant	Intron 1 of 2	5
HRG-AS1	ENST00000626520.2	n.121+10426T>C		intron_variant	Intron 1 of 1	5

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 v4.3

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;