rs2150927

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445829.1. 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
	PFN1P11	ENST00000445829.1	TSL:6	n.291-1457C>T		intron	N/A

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

African (AFR) AF: 0.368 AC: 15245 AN: 41480

American (AMR) AF: 0.393 AC: 6010 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2907 AN: 5172

South Asian (SAS) AF: 0.352 AC: 1699 AN: 4822

European-Finnish (FIN) AF: 0.354 AC: 3740 AN: 10564

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27176 AN: 67988

Other (OTH) AF: 0.391 AC: 825 AN: 2112

Alfa AF: 0.398 Hom.: 1563

Bravo AF: 0.393

Asia WGS AF: 0.411 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.81
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2150927; hg19: chr10-104599323;