rs6984550

Variant names:

• chr8-132545146-A-G
• rs6984550
• ENST00000648355.1:n.1602-11966T>C

Variant summary

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

The ENST00000648355.1(HPYR1):​n.1602-11966T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,094 control chromosomes in the GnomAD database, including 7,634 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 0.27 (7634 hom., cov: 33)
• Consequence: HPYR1 ENST00000648355.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HPYR1	ENST00000648355.1	n.1602-11966T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40920 AN: 151976 Hom.: 7616 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.269 AC: 40974 AN: 152094 Hom.: 7634 Cov.: 33 AF XY: 0.261 AC XY: 19434 AN XY: 74378

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.259

Alfa AF: 0.213 Hom.: 892

Bravo AF: 0.287

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6984550; hg19: chr8-133557393;