chr8-132513122-C-T

Variant names:

• chr8-132513122-C-T
• rs17602731
• ENST00000648355.1:n.1933+2181G>A

Variant summary

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

The ENST00000648355.1(HPYR1):​n.1933+2181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,064 control chromosomes in the GnomAD database, including 5,562 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 0.26 (5562 hom., cov: 33)
• Consequence: HPYR1 ENST00000648355.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPYR1	ENST00000648355.1		n.1933+2181G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38955 AN: 151948 Hom.: 5560 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.256 AC: 38960 AN: 152064 Hom.: 5562 Cov.: 33 AF XY: 0.259 AC XY: 19285 AN XY: 74324

African (AFR) AF: 0.129 AC: 5371 AN: 41480

American (AMR) AF: 0.281 AC: 4283 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3470

East Asian (EAS) AF: 0.128 AC: 662 AN: 5166

South Asian (SAS) AF: 0.402 AC: 1933 AN: 4806

European-Finnish (FIN) AF: 0.301 AC: 3181 AN: 10584

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21493 AN: 67984

Other (OTH) AF: 0.272 AC: 575 AN: 2114

Alfa AF: 0.301 Hom.: 2403

Bravo AF: 0.243

Asia WGS AF: 0.260 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs17602731; hg19: chr8-133525369;