9-107543834-C-A

Variant names:

• chr9-107543834-C-A
• rs10759243
• ENST00000771090.1:n.113-121G>T

Variant summary

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

The ENST00000771090.1(ENSG00000300342):​n.113-121G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,966 control chromosomes in the GnomAD database, including 13,929 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 0.40 (13929 hom., cov: 33)
• Consequence: ENSG00000300342 ENST00000771090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 73 publications found

Genes affected

ENSG00000300342 (HGNC:):

PPIAP88 (HGNC:53712): (peptidylprolyl isomerase A pseudogene 88)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771090.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300342	ENST00000771090.1		n.113-121G>T		intron	N/A
	PPIAP88	ENST00000422463.1	TSL:6	n.-218G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61274 AN: 151848 Hom.: 13889 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.401

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.404 AC: 61370 AN: 151966 Hom.: 13929 Cov.: 33 AF XY: 0.407 AC XY: 30223 AN XY: 74270

African (AFR) AF: 0.611 AC: 25360 AN: 41472

American (AMR) AF: 0.392 AC: 5975 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1268 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2358 AN: 5160

South Asian (SAS) AF: 0.393 AC: 1893 AN: 4812

European-Finnish (FIN) AF: 0.325 AC: 3424 AN: 10546

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19784 AN: 67944

Other (OTH) AF: 0.404 AC: 852 AN: 2110

Alfa AF: 0.330 Hom.: 18602

Bravo AF: 0.420

Asia WGS AF: 0.454 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.48
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10759243; hg19: chr9-110306115; COSMIC: COSV69656636;