chr8-132507817-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648355.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPYR1	ENST00000648355.1		n.*145G>A		downstream_gene	N/A

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 v4.9

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;