rs2150927

Variant names:

• chr10-102839566-G-A
• rs2150927
• ENST00000445829.1:n.291-1457C>T

Variant summary

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

The ENST00000445829.1(PFN1P11):​n.291-1457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,086 control chromosomes in the GnomAD database, including 11,711 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 0.39 (11711 hom., cov: 33)
• Consequence: PFN1P11 ENST00000445829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

PFN1P11 (HGNC:42994): (profilin 1 pseudogene 11)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PFN1P11	ENST00000445829.1	n.291-1457C>T		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59222 AN: 151968 Hom.: 11699 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.390 AC: 59277 AN: 152086 Hom.: 11711 Cov.: 33 AF XY: 0.387 AC XY: 28787 AN XY: 74336

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.391

Alfa AF: 0.399 Hom.: 1506

Bravo AF: 0.393

Asia WGS AF: 0.411 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2150927; hg19: chr10-104599323;