chr5-56275759-A-G

Variant names:

• chr5-56275759-A-G
• rs6895344
• ENST00000515236.1:n.872T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ENSG00000308414 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515236.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMC1P4	ENST00000515236.1	TSL:6	n.872T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000308414	ENST00000833855.1		n.85-5374T>C		intron	N/A

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

African (AFR) AF: 0.220 AC: 4619 AN: 21008

American (AMR) AF: 0.307 AC: 13267 AN: 43284

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 7637 AN: 21864

East Asian (EAS) AF: 0.331 AC: 12178 AN: 36806

South Asian (SAS) AF: 0.413 AC: 30030 AN: 72776

European-Finnish (FIN) AF: 0.330 AC: 15354 AN: 46564

Middle Eastern (MID) AF: 0.345 AC: 1254 AN: 3640

European-Non Finnish (NFE) AF: 0.271 AC: 143142 AN: 528926

Other (OTH) AF: 0.292 AC: 11444 AN: 39188

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

African (AFR) AF: 0.225 AC: 9315 AN: 41428

American (AMR) AF: 0.275 AC: 4203 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5170

South Asian (SAS) AF: 0.401 AC: 1924 AN: 4798

European-Finnish (FIN) AF: 0.331 AC: 3491 AN: 10554

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18432 AN: 67958

Other (OTH) AF: 0.273 AC: 575 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.84
DANN	Benign	0.19
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs6895344; hg19: chr5-55571586;