10-113482772-T-G

Position:

• chr10-113482772-T-G

Variant summary

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

The ENST00000658845.1(ENSG00000286289):​n.2908A>C 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: ENSG00000286289 ENST00000658845.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

Genes affected

PPIAP39 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107984270	XR_001747591.2	n.3183A>C		non_coding_transcript_exon_variant	2/2
LOC107984270	XR_001747592.2	n.3660A>C		non_coding_transcript_exon_variant	2/2
PPIAP39		n.113482772T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPIAP39	ENST00000415988.1	n.157T>G		non_coding_transcript_exon_variant	1/1	6
ENSG00000286289	ENST00000658845.1	n.2908A>C		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR exome AF: 0.754

Gnomad4 AMR exome AF: 0.861

Gnomad4 ASJ exome AF: 0.737

Gnomad4 EAS exome AF: 0.907

Gnomad4 SAS exome AF: 0.789

Gnomad4 FIN exome AF: 0.772

Gnomad4 NFE exome AF: 0.732

Gnomad4 OTH exome AF: 0.762

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

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.740

Alfa AF: 0.710 Hom.: 3872

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1046528; hg19: chr10-115242531;