8-132513122-C-T

Position:

• chr8-132513122-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648355.1(HPYR1):​n.1933+2181G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

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

LOC124902028 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902028	XR_007061116.1	n.267+2181G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HPYR1	ENST00000648355.1	n.1933+2181G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.272

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17602731; hg19: chr8-133525369;