rs1046528

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-113482772-T-A
• chr10-113482772-T-C
• chr10-113482772-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000415988.1(PPIAP39):​n.157T>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 0.0000263 in 152,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000054 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 151988 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000967

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000541 AC: 1 AN: 184844 Hom.: 0 Cov.: 0 AF XY: 0.00000930 AC XY: 1 AN XY: 107472

African (AFR) AF: 0.000252 AC: 1 AN: 3970

American (AMR) AF: 0.00 AC: 0 AN: 14190

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3322

East Asian (EAS) AF: 0.00 AC: 0 AN: 7210

South Asian (SAS) AF: 0.00 AC: 0 AN: 28116

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16830

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1566

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 100960

Other (OTH) AF: 0.00 AC: 0 AN: 8680

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 152106 Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4 AN XY: 74368

African (AFR) AF: 0.0000964 AC: 4 AN: 41476

American (AMR) AF: 0.00 AC: 0 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68010

Other (OTH) AF: 0.00 AC: 0 AN: 2110

Alfa AF: 0.00 Hom.: 4084

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.5
DANN	Benign	0.25
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;