rs2150927

Positions:

• chr10-102839566-G-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PFN1P11	ENST00000445829.1	n.291-1457C>T		intron_variant, non_coding_transcript_variant

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;