rs13039601

Positions:

• chr20-54224495-A-G

Variant summary

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

The ENST00000441080.2(PFDN4):​c.*62+196A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,228 control chromosomes in the GnomAD database, including 1,518 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 0.12 (1518 hom., cov: 31)
• Consequence: PFDN4 ENST00000441080.2 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PFDN4	ENST00000441080.2	c.*62+196A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18927 AN: 152110 Hom.: 1518 Cov.: 31

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.124 AC: 18920 AN: 152228 Hom.: 1518 Cov.: 31 AF XY: 0.122 AC XY: 9111 AN XY: 74404

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0888

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.132

Alfa AF: 0.165 Hom.: 2915

Bravo AF: 0.116

Asia WGS AF: 0.0170 AC: 60 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	2.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13039601; hg19: chr20-52841034;