rs2585417

Variant names:

• chr20-54227260-G-A
• rs2585417
• ENST00000441080.2:n.*63-693G>A

Variant summary

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

The ENST00000441080.2(PFDN4):​n.*63-693G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,858 control chromosomes in the GnomAD database, including 24,549 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 0.56 (24549 hom., cov: 31)
• Consequence: PFDN4 ENST00000441080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

PFDN4 (HGNC:8868): (prefoldin subunit 4) This gene encodes a member of the prefoldin beta subunit family. The encoded protein is one of six subunits of prefoldin, a molecular chaperone complex that binds and stabilizes newly synthesized polypeptides, thereby allowing them to fold correctly. The complex, consisting of two alpha and four beta subunits, forms a double beta barrel assembly with six protruding coiled-coils. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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
PFDN4	ENST00000441080.2	n.*63-693G>A		intron_variant	Intron 5 of 5	5		ENSP00000432441.1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84624 AN: 151740 Hom.: 24502 Cov.: 31

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.558 AC: 84720 AN: 151858 Hom.: 24549 Cov.: 31 AF XY: 0.554 AC XY: 41101 AN XY: 74208

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.529

Alfa AF: 0.515 Hom.: 20024

Bravo AF: 0.554

Asia WGS AF: 0.419 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2585417; hg19: chr20-52843799;