rs10913237

chr1-176661280-G-A

Variant summary

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

The NM_020318.3(PAPPA2):c.1992-9690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,846 control chromosomes in the GnomAD database, including 2,464 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 0.17 (2464 hom., cov: 31)
• Consequence: PAPPA2 NM_020318.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

Genes affected

PAPPA2 (HGNC:14615): (pappalysin 2) This gene encodes a member of the pappalysin family of metzincin metalloproteinases. The encoded protein cleaves insulin-like growth factor-binding protein 5 and is thought to be a local regulator of insulin-like growth factor (IGF) bioavailability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAPPA2	NM_020318.3	c.1992-9690G>A		intron_variant		ENST00000367662.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAPPA2	ENST00000367662.5	c.1992-9690G>A		intron_variant		1	NM_020318.3	P1
PAPPA2	ENST00000367661.7	c.1992-9690G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26499 AN: 151728 Hom.: 2463 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.00252

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.175 AC: 26502 AN: 151846 Hom.: 2464 Cov.: 31 AF XY: 0.172 AC XY: 12793 AN XY: 74176

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.00272

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.181

Alfa AF: 0.178 Hom.: 1185

Bravo AF: 0.171

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.70
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10913237; hg19: chr1-176630416;