rs17724534

Positions:

• chr10-102845764-C-T

Variant summary

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

The ENST00000631443.1(ENSG00000282772):​n.559G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 318,148 control chromosomes in the GnomAD database, including 2,249 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 0.090 (797 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1452 hom.)
• Consequence: ENSG00000282772 ENST00000631443.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621

Genes affected

PTGES3P4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGES3P4		n.102845764C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGES3P4	ENST00000426243.2	n.170C>T		non_coding_transcript_exon_variant	1/1	6
ENSG00000282772	ENST00000631443.1	n.559G>A		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13738 AN: 152180 Hom.: 798 Cov.: 32

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0750

GnomAD4 exome AF: 0.124 AC: 20622 AN: 165850 Hom.: 1452 Cov.: 0 AF XY: 0.120 AC XY: 11040 AN XY: 91794

Gnomad4 AFR exome AF: 0.0213

Gnomad4 AMR exome AF: 0.0903

Gnomad4 ASJ exome AF: 0.0747

Gnomad4 EAS exome AF: 0.00326

Gnomad4 SAS exome AF: 0.0862

Gnomad4 FIN exome AF: 0.149

Gnomad4 NFE exome AF: 0.141

Gnomad4 OTH exome AF: 0.133

GnomAD4 genome AF: 0.0902 AC: 13730 AN: 152298 Hom.: 797 Cov.: 32 AF XY: 0.0903 AC XY: 6723 AN XY: 74464

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0787

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0844 Hom.: 135

Bravo AF: 0.0813

Asia WGS AF: 0.0340 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17724534; hg19: chr10-104605521;