rs3130350

Variant names:

• chr6-30360062-G-T
• rs3130350

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 0.0693 in 152,154 control chromosomes in the GnomAD database, including 502 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 0.069 (502 hom., cov: 32)
• Consequence: UBQLN1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 34 publications found

Genes affected

UBQLN1P1 (HGNC:21633): (ubiquilin 1 pseudogene 1)

HCG19P (HGNC:31336): (HLA complex group 19 pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBQLN1P1		n.30360062G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG19P	ENST00000448756.1	n.-151C>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10534 AN: 152036 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0342

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0693 AC: 10537 AN: 152154 Hom.: 502 Cov.: 32 AF XY: 0.0642 AC XY: 4775 AN XY: 74372

African (AFR) AF: 0.0448 AC: 1859 AN: 41500

American (AMR) AF: 0.0341 AC: 521 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0256 AC: 89 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4820

European-Finnish (FIN) AF: 0.0693 AC: 734 AN: 10586

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7078 AN: 67984

Other (OTH) AF: 0.0469 AC: 99 AN: 2112

Alfa AF: 0.0921 Hom.: 1920

Bravo AF: 0.0660

Asia WGS AF: 0.00549 AC: 20 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	1.5
DANN	Benign	0.19
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs3130350; hg19: chr6-30327839;