rs2673582

Variant names:

• chr8-132507817-C-T
• rs2673582
• ENST00000648355.1:n.*145G>A

Variant summary

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

The ENST00000648355.1(HPYR1):​n.*145G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,974 control chromosomes in the GnomAD database, including 22,449 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 0.54 (22449 hom., cov: 32)
• Consequence: HPYR1 ENST00000648355.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 3 publications found

Genes affected

HPYR1 (HGNC:16071): (Helicobacter pylori responsive 1)

LOC124902028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902028	XR_007061116.1	n.*18G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HPYR1	ENST00000648355.1	n.*145G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81682 AN: 151856 Hom.: 22425 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.538 AC: 81735 AN: 151974 Hom.: 22449 Cov.: 32 AF XY: 0.536 AC XY: 39787 AN XY: 74270

African (AFR) AF: 0.452 AC: 18726 AN: 41436

American (AMR) AF: 0.584 AC: 8932 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3466

East Asian (EAS) AF: 0.609 AC: 3149 AN: 5170

South Asian (SAS) AF: 0.417 AC: 2002 AN: 4806

European-Finnish (FIN) AF: 0.598 AC: 6310 AN: 10554

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.580 AC: 39418 AN: 67948

Other (OTH) AF: 0.523 AC: 1102 AN: 2108

Alfa AF: 0.548 Hom.: 3008

Bravo AF: 0.537

Asia WGS AF: 0.466 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs2673582; hg19: chr8-133520064;