5-56275759-A-G

Position:

• chr5-56275759-A-G

Variant summary

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

The ENST00000515236.1(PSMC1P4):​n.872T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.29 in 966,010 control chromosomes in the GnomAD database, including 42,050 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 0.27 (5712 hom., cov: 31)
  • Exomes 𝑓: 0.29 (36338 hom.)
• Consequence: PSMC1P4 ENST00000515236.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.79

Genes affected

PSMC1P4 (HGNC:39779): (proteasome 26S subunit, ATPase 1 pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 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
PSMC1P4	ENST00000515236.1	n.872T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41007 AN: 151836 Hom.: 5704 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.272

GnomAD4 exome AF: 0.293 AC: 238925 AN: 814056 Hom.: 36338 Cov.: 11 AF XY: 0.298 AC XY: 128651 AN XY: 431084

Gnomad4 AFR exome AF: 0.220

Gnomad4 AMR exome AF: 0.307

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.331

Gnomad4 SAS exome AF: 0.413

Gnomad4 FIN exome AF: 0.330

Gnomad4 NFE exome AF: 0.271

Gnomad4 OTH exome AF: 0.292

GnomAD4 genome AF: 0.270 AC: 41038 AN: 151954 Hom.: 5712 Cov.: 31 AF XY: 0.275 AC XY: 20418 AN XY: 74258

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.273

Alfa AF: 0.259 Hom.: 1152

Bravo AF: 0.263

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.84
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6895344; hg19: chr5-55571586;