chr10-102845764-C-T

Variant names:

• chr10-102845764-C-T
• rs17724534
• ENST00000426243.2:n.170C>T

Variant summary

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

The ENST00000426243.2(PTGES3P4):​n.170C>T 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: PTGES3P4 ENST00000426243.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621
• Publications: 4 publications found

Genes affected

PTGES3P4 (HGNC:43825): (prostaglandin E synthase 3 pseudogene 4)

ENSG00000282772 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426243.2. 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
	PTGES3P4	ENST00000426243.2	TSL:6	n.170C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000282772	ENST00000631443.1	TSL:4	n.559G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000282772	ENST00000744031.1		n.660G>A		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.0213 AC: 46 AN: 2160

American (AMR) AF: 0.0903 AC: 406 AN: 4494

Ashkenazi Jewish (ASJ) AF: 0.0747 AC: 270 AN: 3616

East Asian (EAS) AF: 0.00326 AC: 9 AN: 2762

South Asian (SAS) AF: 0.0862 AC: 2673 AN: 31016

European-Finnish (FIN) AF: 0.149 AC: 3395 AN: 22724

Middle Eastern (MID) AF: 0.0625 AC: 37 AN: 592

European-Non Finnish (NFE) AF: 0.141 AC: 12755 AN: 90754

Other (OTH) AF: 0.133 AC: 1031 AN: 7732

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

African (AFR) AF: 0.0233 AC: 967 AN: 41582

American (AMR) AF: 0.0785 AC: 1202 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.0787 AC: 380 AN: 4828

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9093 AN: 68016

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0825 Hom.: 135

Bravo AF: 0.0813

Asia WGS AF: 0.0340 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.2
DANN	Benign	0.63
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs17724534; hg19: chr10-104605521;