chr3-90214906-C-T

Variant names:

• chr3-90214906-C-T
• rs9878394

Variant summary

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

The variant allele was found at a frequency of 0.0619 in 152,104 control chromosomes in the GnomAD database, including 399 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 0.062 (399 hom., cov: 32)
• Consequence: PROS2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

Genes affected

PROS2P (HGNC:9458): (protein S (beta) pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PROS2P		n.90214906C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PROS2P	ENST00000474651.1	n.1243+690G>A		intron_variant	Intron 10 of 13	6

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9420 AN: 151986 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0619 AC: 9416 AN: 152104 Hom.: 399 Cov.: 32 AF XY: 0.0582 AC XY: 4329 AN XY: 74350

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.0128

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.0588

Gnomad4 NFE AF: 0.0953

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0664 Hom.: 133

Bravo AF: 0.0602

Asia WGS AF: 0.0220 AC: 77 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9878394; hg19: chr3-90264056;