rs13039601

Variant names:

• chr20-54224495-A-G
• rs13039601
• ENST00000441080.2:n.*62+196A>G

Variant summary

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

The ENST00000441080.2(PFDN4):​n.*62+196A>G variant causes a intron 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PFDN4	ENST00000441080.2	n.*62+196A>G		intron_variant	Intron 5 of 5	5		ENSP00000432441.1

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;