10-113482772-T-G

Variant names:

• chr10-113482772-T-G
• rs1046528
• ENST00000415988.1:n.157T>G

Variant summary

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

The ENST00000415988.1(PPIAP39):​n.157T>G 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 0.758 in 336,344 control chromosomes in the GnomAD database, including 97,049 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 0.75 (42955 hom., cov: 32)
  • Exomes 𝑓: 0.76 (54094 hom.)
• Consequence: PPIAP39 ENST00000415988.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 5 publications found

Genes affected

PPIAP39 (HGNC:53663): (peptidylprolyl isomerase A pseudogene 39)

ENSG00000286289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984270	XR_001747591.2	n.3183A>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC107984270	XR_001747592.2	n.3660A>C		non_coding_transcript_exon_variant	Exon 2 of 2
PPIAP39		n.113482772T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIAP39	ENST00000415988.1	n.157T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000286289	ENST00000658845.2	n.3093A>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000286289	ENST00000793017.1	n.438A>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114180 AN: 151940 Hom.: 42914 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.740

GnomAD4 exome AF: 0.764 AC: 140722 AN: 184286 Hom.: 54094 Cov.: 0 AF XY: 0.765 AC XY: 81951 AN XY: 107148

African (AFR) AF: 0.754 AC: 2990 AN: 3966

American (AMR) AF: 0.861 AC: 12199 AN: 14166

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2438 AN: 3308

East Asian (EAS) AF: 0.907 AC: 6532 AN: 7204

South Asian (SAS) AF: 0.789 AC: 22134 AN: 28040

European-Finnish (FIN) AF: 0.772 AC: 12943 AN: 16768

Middle Eastern (MID) AF: 0.780 AC: 1220 AN: 1564

European-Non Finnish (NFE) AF: 0.732 AC: 73674 AN: 100620

Other (OTH) AF: 0.762 AC: 6592 AN: 8650

GnomAD4 genome AF: 0.752 AC: 114275 AN: 152058 Hom.: 42955 Cov.: 32 AF XY: 0.756 AC XY: 56235 AN XY: 74350

African (AFR) AF: 0.744 AC: 30863 AN: 41462

American (AMR) AF: 0.806 AC: 12296 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2571 AN: 3470

East Asian (EAS) AF: 0.900 AC: 4652 AN: 5170

South Asian (SAS) AF: 0.795 AC: 3829 AN: 4816

European-Finnish (FIN) AF: 0.771 AC: 8154 AN: 10576

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.729 AC: 49540 AN: 67998

Other (OTH) AF: 0.740 AC: 1559 AN: 2108

Alfa AF: 0.711 Hom.: 4084

Bravo AF: 0.753

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.5
DANN	Benign	0.43
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1046528; hg19: chr10-115242531;